I think this should work just fine:
Lets start with everything (computers A&B, NAS, pendrive) in sync, then modify something while the pendrive is at A and move with the pendrive to B. If no sync happens before the pendrive is inserted, B will scan the pendrive, find the changes and update its index. When they later get connected, this will be registered as a conflict. As both sides of the conflict (A, B) have the identical file, this will be resolved silently. This should always be the case, as the folder on B is paused until the pendrive is plugged in (folder marker is missing). Even if some index exchange did happen before, there would still be nothing to be done as files are identical.
I might be missing something, so try it out and tell us whether it actually worked.