unfortunately I hadn't made regular backups, so I had to make a decision, restore from a backup made in April 2012 or delete duplicates using the 'find duplicates' facility in FTM (advice from support centre). I chose the latter, & like you I have spent Christmas deleting duplicated people, about 3,500 so far, but still another 2,000 to go! Totally mind numbing, but just have to keep plodding on.
I am certain my duplicates were made every time a sync failed, not realising what was happening I just carried on trying to sync the tree, which I did many, many times. I would be interested to hear how you got on with syncing.
Moral of this story, take regular backups, & maybe find some other software that doesn't wreck your tree?