Tommy - if you do all your work in ancestry, you don't have source templates or fact notes, media notes, etc., to lose since those are FTM features. I can assure you that the problem you have with the sources/citations is because you do most of your work on ancestry and ancestry has created multiple source groups in FTM (I believe it's the new merge tool for attaching records that causes this).
When you allow the sync, you will see that many of the duplicated spruce groups are combined and all your citations are still present. If you look at the sync report, you will see no citations were deleted. Only sources. Look at some of those on ancestry and you will see there is still a citation... That's because the citation changed to the correct source group and the empty source group was deleted (so to speak). That's why you have so many changed citations. The underlying source it is connected to was changed. It's a fix... even though it's kind of scary, it's okay to sync.