iOS Backup: Restore single program's settings?
Theoretically, it is possible to replace parts of the backup package, but in practice, I have no real success with that plan. Often the format iTunes uses to store the data changes with versions of iTunes and editing files under a database's nose can lead to corruption.

It's easier for me to connect both devices and quit the program to make sure it's a clean boot when you resume the app. Then I use PhoneView to read the preferences from the app bundle on the correct device and replace that folder on the bad device. This way if things crash, you still have pristine backups in iTunes to restore things.