Q:

What happened to the Future Flash?

In The Flash, the Flash from the future traveled back in time to stop the Reverse-Flash from killing his mother. He failed, but where did he go? The Reverse-Flash was stuck in past, so he killed and took the appearance of Doctor Harrison Wells. In his hidden room we see holograms of newspapers from the year 2024 with article about the Flash gone missing. So he didn't travel back to the future. Where is the future Flash?  

A:

We don't know. 2 seasons in, they haven't brought it up.
We don't know the extent of Eobard Thawne's supercomputer Gideon's ability to scan the timelines.
We do know is that while the Reverse-Flash is faster than the Flash most of the time, the Flash does not have his issues with time travel. Eobard, in the multiple times we see him time-travel regardless of how, seems to loose his connection to the Speed-Force. Flash, the multiple times we see him time-travel, can do it without any loss of powers.
And due to the constant inconsistencies in how the show handles time-travel (See Why wasn't the timeline affected any further from the events in the season 1 finale?) we don't really know how the show attempts to handle it.
We do know that comic Barry Allen, prior to the DC Crisis of Infinite Earths, during the "Trial of the Flash" in the 80's, essentially leaves the current time and ends up living in the 30th Century, with a reincarnated Iris.
So possibly, after saving his 10 year old self, Future Barry gets sent forward significantly into the future to the 25th or 30th century, Or he returns in 2024 and Gideon simply doesn't know.
Since we only have Eobard's word that he created the particle accelerator explosion 15 years earlier then it normally happened, turning Barry into the Flash much earlier, or if any of the events that shaped Barry into the future Barry that disappeared in 2024, we don't know if that timeline exists as that Barry knew it. The future Flash could be a Timeline Remnant of some sort that disappeared.

