Everything doubled after update from 1.0.9 to 1.5b1
I was using the sync preview on one of my computers and kept my main computer on 1.0.9. After updating this computer to 1.5.b1 and syncing to the same account I was using on the other computer I got hundereds of duplicate entries and collections.
If you have a backup of the database you want on both machines you can revert to that and restore it to the server. If you don't you can seek out the duplicate collections, select all items in them and delete them, then remove the empty duplicate collections.
If the items were duplicated in some other strange series of events try sorting them by date added, and deleting all the duplicate items as noted by the later date added.
Reverting to a back-up and replacing the server-sided database worked.