I have yet, to have any of what you say WILL happen, happen to me. Nothing has been lost, no filename re-do's. Have I restored files, certainly, many times.
What YOU are proposing is NOT for the 'normal' user of Family Tree Maker. An experienced COMPUTER user, probably would be comfortable doing what you suggest, but I wouldn't do it.
But, then again YOU are the EXPERT here.
Will something happen to the Sync Feature IF you do a Restore, certainly. You would have to re-invite anyone who you invited to your AMT. Some data would be lost, like the comments in the AMT. But IF I had comments there, in the AMT, I would certainly get them into my FTM2012 file as the comments were made, but they won't be in the Sync Feature anyway.
The Restore does NOT looks Tasks, does NOT loose Saved Reports, does NOT loose Media Categories.
I forgot, YOU are the Expert.
I'll step aside