Out of order to your points, but:
1. I always compact after doing a full backup. And I try to do a full backup daily. Having been through too many database rebuilds from data loss I am a bit paranoid that way.
2. I have way too many places that FTM will not recognize (old locations no longer around), and so I do place name resolves as I find them as it were. (My database is 29K people). Syncing is part of my "backup systems" as it were, since I know that I have at least a chance at partial data recovery from a fully synced file online.
3. Both places were resolved. I was worried since Boone was not showing up as an option under the place hierarchy at all (places will show up as greyed out in the hierarchy if they exist and you do not use them). However .... (see 4 below)
4. I went into the "corrupted" file and changed the location to Boone County. At first it did not recognize it and I resolved it. Now it shows up properly in the place name hierarchy. It might not have been corrupted so much as confused, although how FTM lost a place name and overwrote it I do not understand at all.
Looks like I can manually change all the places for that couple back to what they should have been -- I just hope it was only that county that got messed up. I really have too many people to check everyone.
Then later on I should look into if I have some bad sectors on this disk (that caused said blue screen of death).