My way to deal with this is to make sure to keep regular, multiple backups. I feel better knowing that the data is both in FTM on my computer and online. I regularly back up the FTM version and periodically download a copy of the GEDCOM from the online tree in Tree Settings.
When I have had problems with sync, I've chosen to unlink, delete the FTM tree, and then download the online tree into FTM once again (because doing it in this direction preserves Member Connect links, reviewed hints, and my invitations to family contributors). It's a nuisance, but it works.
I also like that I can cancel Sync temporarily when FTM starts up. That way if an error occurs while I'm doing data entry in the online tree, I can go into the FTM version and refer to what was there before the change.