Originally Posted by DjNDB
I am not 100% sure how steam cloud will react to the modifications.
I would make a backup copy of your working savegame folder, and then enable steam cloud, to see what happens the next time it syncs.
Figured I'd let anyone interested in this problem know that I've been playing the game on and off over the past few days with the steam cloud enabled and haven't had any more issues. I've made it to Episode 4 without a problem.
Thanks again for the help.