I just had to re-download my synced Ancestry.com database to FTM 2012 to resolve a sync corruption issue. (No known reason why it got corrupted but that's another issue). After a quick inspection, it appears that the family tree, facts for people, references, and media came back OK. But some other information didn't. Most of the missing information appears to be related to "features" that have been added to FTM in the last two years but haven't been implemented at Ancestry.com. In particular;
(1) FTM has a "PLAN" tab where you can manage your todo list. None of this came back.
(2) With 2012, FTM has totally redone its location database. I like the implementation and have spent many days (yes days) cleaning up my locations so that they fit the new format. In many cases, I had to manually enter latitude and longitude coordinates to "help" the location database find the particular location. All of this was lost when I recreated my FTM file from the Ancestry.com database.
Come on Ancestry management!!!! Don't push a feature on one platform if you aren't ready to implement it across your product line. This is especially irritating because Ancestry is selling their on-line sync feature as a way to "backup" your FTM database. It isn't a backup, its a partial copy. Even worse, the sync process is creating multiple opportunities to corrupt your local file.