I'm about 70% sure, based on my own anecdote and the experience of my friends, that if you have a sync fainted and you put that fainted sync in a box and then take it out that it not longer syncs until you revive it and faint it again.
Replication:
Faint sync
Put fainted sync in PC box
Take Sync out
Sync doesnt work
Seemingly fixed upon revive and fainting the pokemon again.
I could just be crazy but I'm pretty sure this is prevalent. Also if this is a known issue then I didnt know what to search. I searched a couple things looking for a similar issue.