How do you copy the apps and put them in another directory? Great suggestion, didn't know that was even possible.
Don't you have a backup of the app somewhere?
When my iPhone does a backup to my computer, a grab a copy of all the apps and save them off to a different directory so I can copy them back if I need to. I have zero faith in Apple's sync logic. It seems to have more holes in it than Bonnie and Clyde.