user17096: I have burned out a few Pro Micro clones now. Initially I ran them using a 12VDC external raw power supply but two Pro Micro clones burned out pretty quickly this way. Another thread suggested that the Pro Micro clones use regulators that are not very robust. Since then, I've been using just USB power for my 5V/16MHz Pro Micro clones.
The third clone has been working fine on USB power only. I estimate that I uploaded a sketch I was working on about a dozen times. Suddenly the RxLED stayed lit and I can't upload to it anymore.
When I plug it in, Windows assigns a COM port successfully. The Arduino IDE sees the port and I can select it. This tells me the Pro Micro is not entirely dead. When I enable verbose mode for uploading in the Arduino IDE, here's what I get:
Sketch uses 3,914 bytes (13%) of program storage space. Maximum is 28,672 bytes.
Global variables use 148 bytes (5%) of dynamic memory, leaving 2,412 bytes for local variables. Maximum is 2,560 bytes.
Forcing reset using 1200bps open/close on port COM3
PORTS {COM3, } / {COM3, } => {}
[repeating 19 more times]
Uploading using selected port: COM3
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Users\Bartman\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.2/avrdude.conf -v -patmega32u4 -cavr109 -PCOM3 -b57600 -D -Uflash:w:C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:i 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Users\Bartman\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.2/avrdude.conf"

         Using Port                    : COM3
         Using Programmer              : avr109
         Overriding Baud Rate          : 57600
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : butterfly
         Description     : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .

and after some time:
avrdude: butterfly_recv(): programmer is not responding
Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.

On my working Pro Micro clone, I get the following after instead:
Found programmer: Id = "CATERIN"; type = S
    Software Version = 1.0; No Hardware Version given.
Programmer supports auto addr increment.
Programmer supports buffered memory access with buffersize=128 bytes.

Programmer supports the following devices:
    Device code: 0x44

avrdude: devcode selected: 0x44
avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% -0.00s

avrdude: Device signature = 0x1e9587
avrdude: reading input file "C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex"
avrdude: writing flash (3914 bytes):

Writing | ################################################## | 100% 0.30s

avrdude: 3914 bytes of flash written
avrdude: verifying flash memory against C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:
avrdude: load data flash data from input file C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:
avrdude: input file C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex contains 3914 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.04s

avrdude: verifying ...
avrdude: 3914 bytes of flash verified

avrdude done.  Thank you.

On the now non-functional one, I tried using a jumper from RST to GND, tapping this twice quickly in succession and uploading from the IDE in an attempt to recover the Pro Micro but this doesn't work.
I don't think it's a bootloader problem since the Pro Micro does get a COM port assigned to it but never-the-less, I tried burning a new bootloader from my working Pro Micro. Here's my Pro Micro to Pro Micro wiring:

In the IDE, I've selected:

Board: SparkFun Pro Micro
  Processor: ATmega32U4 (5V, 16 MHz)
  Port: [current COM port of working Pro Micro]
  Programmer: Arduino as ISP

But when I select Tools->Burn Bootloader, I get the following error:
Arduino: 1.6.7 (Windows 10), Board: "SparkFun Pro Micro, ATmega32U4 (5V, 16 MHz)"

C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Users\Bart_S\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.3/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM6 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xCB:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Users\Bart_S\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.3/avrdude.conf"

         Using Port                    : COM6
         Using Programmer              : stk500v1
         Overriding Baud Rate          : 19200
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0x03

avrdude done.  Thank you.

Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.

Is it permanently damaged? What are the next steps to troubleshoot this Pro Micro clone?

user9962: To make things simpler, try flashing the Pro Micro firmware with another UNO (or compatible) hardware. I prefer an UNO clone with CH340 chip or a pro mini with a FTDI cable. Just to keep things simple.
Flash the UNO with Arduiono as ISP sketch. Use connection guidance from Arduino tutorial:
Using an Arduino as an AVR ISP

Once this is done, AVRDUDE will see the source Arduino as AVR ISP and you can flash the firmware on the target Arduino.
You can also use this post for guidance as well.

user17096: After many hours of unsuccessful bootloader reprogramming attempts, I was able to revive the Pro Micro by trying different timing of double tapping RST while the IDE was compiling/uploading a sketch. After several attempts the Pro Micro suddenly took a sketch and seems to be working now. Not sure how long it will stay this way or how often I will loose it and have to go through these shenanigans again.
Thanks to all for the help.

17096: <p>I have burned out a few Pro Micro clones now. Initially I ran them using a 12VDC external raw power supply but two Pro Micro clones burned out pretty quickly this way. Another thread suggested that the Pro Micro clones use regulators that are not very robust. Since then, I've been using just USB power for my 5V/16MHz Pro Micro clones.</p>

<p>The third clone has been working fine on USB power only. I estimate that I uploaded a sketch I was working on about a dozen times. Suddenly the RxLED stayed lit and I can't upload to it anymore.</p>

<p>When I plug it in, Windows assigns a COM port successfully. The Arduino IDE sees the port and I can select it. This tells me the Pro Micro is not entirely dead. When I enable verbose mode for uploading in the Arduino IDE, here's what I get:</p>

<pre><code>Sketch uses 3,914 bytes (13%) of program storage space. Maximum is 28,672 bytes.
Global variables use 148 bytes (5%) of dynamic memory, leaving 2,412 bytes for local variables. Maximum is 2,560 bytes.
Forcing reset using 1200bps open/close on port COM3
PORTS {COM3, } / {COM3, } =&gt; {}
[repeating 19 more times]
Uploading using selected port: COM3
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Users\Bartman\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.2/avrdude.conf -v -patmega32u4 -cavr109 -PCOM3 -b57600 -D -Uflash:w:C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:i 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Users\Bartman\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.2/avrdude.conf"

         Using Port                    : COM3
         Using Programmer              : avr109
         Overriding Baud Rate          : 57600
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : butterfly
         Description     : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .
</code></pre>

<p>and after some time:</p>

<pre><code>avrdude: butterfly_recv(): programmer is not responding
Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.
</code></pre>

<p>On my working Pro Micro clone, I get the following after instead:</p>

<pre><code>Found programmer: Id = "CATERIN"; type = S
    Software Version = 1.0; No Hardware Version given.
Programmer supports auto addr increment.
Programmer supports buffered memory access with buffersize=128 bytes.

Programmer supports the following devices:
    Device code: 0x44

avrdude: devcode selected: 0x44
avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% -0.00s

avrdude: Device signature = 0x1e9587
avrdude: reading input file "C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex"
avrdude: writing flash (3914 bytes):

Writing | ################################################## | 100% 0.30s

avrdude: 3914 bytes of flash written
avrdude: verifying flash memory against C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:
avrdude: load data flash data from input file C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex:
avrdude: input file C:\Users\Bartman\AppData\Local\Temp\buildb15cf522f4023b15f86cbd1c900761d6.tmp/sketch_feb15a.ino.hex contains 3914 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.04s

avrdude: verifying ...
avrdude: 3914 bytes of flash verified

avrdude done.  Thank you.
</code></pre>

<p>On the now non-functional one, I tried using a jumper from RST to GND, tapping this twice quickly in succession and uploading from the IDE in an attempt to recover the Pro Micro but this doesn't work.</p>

<p>I don't think it's a bootloader problem since the Pro Micro does get a COM port assigned to it but never-the-less, I tried burning a new bootloader from my working Pro Micro. Here's my Pro Micro to Pro Micro wiring:
<a href="https://i.stack.imgur.com/d6G4t.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/d6G4t.jpg" alt="enter image description here"></a></p>

<p>In the IDE, I've selected:</p>

<blockquote>
  <p>Board: SparkFun Pro Micro<br>
  Processor: ATmega32U4 (5V, 16 MHz)<br>
  Port: [current COM port of working Pro Micro]<br>
  Programmer: Arduino as ISP<br></p>
</blockquote>

<p>But when I select <code>Tools-&gt;Burn Bootloader</code>, I get the following error:</p>

<pre><code>Arduino: 1.6.7 (Windows 10), Board: "SparkFun Pro Micro, ATmega32U4 (5V, 16 MHz)"

C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Users\Bart_S\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.3/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM6 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xCB:m -Uhfuse:w:0xD8:m -Ulfuse:w:0xFF:m 

avrdude: Version 6.0.1, compiled on Apr 15 2015 at 19:59:58
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "C:\Users\Bart_S\AppData\Local\Arduino15\packages\SparkFun\hardware\avr\1.1.3/avrdude.conf"

         Using Port                    : COM6
         Using Programmer              : stk500v1
         Overriding Baud Rate          : 19200
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 1 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 2 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 3 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 4 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 6 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 7 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 8 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 9 of 10: not in sync: resp=0x03
avrdude: stk500_recv(): programmer is not responding
avrdude: stk500_getsync() attempt 10 of 10: not in sync: resp=0x03

avrdude done.  Thank you.

Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.
</code></pre>

<p>Is it permanently damaged? What are the next steps to troubleshoot this Pro Micro clone?</p>
 9962: <p>To make things simpler, try flashing the Pro Micro firmware with another UNO (or compatible) hardware. I prefer an UNO clone with CH340 chip or a pro mini with a FTDI cable. Just to keep things simple.</p>

<p>Flash the UNO with Arduiono as ISP sketch. Use connection guidance from Arduino tutorial:
<a href="https://www.arduino.cc/en/Tutorial/ArduinoISP" rel="nofollow noreferrer">Using an Arduino as an AVR ISP</a></p>

<p><a href="https://i.stack.imgur.com/j6Wh1.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/j6Wh1.png" alt="connection diagram"></a></p>

<p>Once this is done, AVRDUDE will see the source Arduino as <strong>AVR ISP</strong> and you can flash the firmware on the target Arduino.</p>

<p>You can also use <a href="http://blog.bhargavaz.us/2011/08/programming-arduino-bootloader-on-mega8.html" rel="nofollow noreferrer">this post</a> for guidance as well.</p>
 17096: <p>After many hours of unsuccessful bootloader reprogramming attempts, I was able to revive the Pro Micro by trying different timing of double tapping RST while the IDE was compiling/uploading a sketch. After several attempts the Pro Micro suddenly took a sketch and seems to be working now. Not sure how long it will stay this way or how often I will loose it and have to go through these shenanigans again.</p>

<p>Thanks to all for the help.</p>
