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.