I plan to cook a brisket for 48+ hours. However I ordered some liquid smoke online and it wont arrive until the next day. I cant wait for it to arrive or I will not have enough time to finish the brisket.  Is there any problem with cooking the brisket for 24 hours, then opening the sous-vide bag. Adding liquid smoke and then cooking for the remaining 24?  
I would think that it wouldn't be ideal ... but if you work quickly it shouldn't cause too much problem.  (basically, you want to work quickly enough that the meat doesn't cool down significantly).    I'd probably prep the replacement bag before I even took the meat out of the water, and have a towel and scissors ready (pull the bag out, dry the outside, cut it open, dump it into the new bag (with the liquid smoke already in it), seal it, then get it back in the water.  If you're using a vacuum sealer, and not just a zip-top bag, I'd make sure it's warmed up first, too.  Drying the bag might seem like a pendantic step, but it's both to prevent you getting water into the new bag, and to reduce the amount of evaporative cooling. 