Sorry about the confusion. It wasn't just my FTM file that had the problems. The sync errors created duplicates in both FTM and on Ancestry.com. Because FTM has the merge duplicates option, I did the clean-up there, and am now trying to see if I can sync FTM back to Ancestry and erase those duplicates. But I'm starting to think that won't work.
Right now, my tree on Ancestry has about 200-300 people with 3 extra copies. So instead of one John Smith I have 4. Easy enough to fix when it's only a couple of people, but there are hundreds duplicated to that extent.
Ancestry, however, is where I do everything. FTM was really more of a backup to me, and I rarely used it. This all happened because I opened the program by mistake once and it auto-synced, got errors, etc. But because Ancestry is my main tree, I really don't want to trash it and upload FTM's file to it. I'm afraid I'll lose all the Ancestry source links that way.
My question was really when you sync the two programs, will Ancestry see that I've deleted these people and delete them from the online tree as well, or will it keep the duplicates and add them back to FTM, even though FTM's file is the more recent? Am I better off taking the time to delete them manually?
Thanks for the help!