Possibly a little late to the game, but I've seen your problem before. The problem is most likely your settings. Your PC should be the left folder and the NAS the right folder, and the sync option should be
Echo, NOT Synchronize. Synchronize works both ways, so if it sees no files on the right (NAS), it will assume you want no files on the left and delete everything there. Echo, on the other hand, only works from left to right, so
any changes made on the left will be echoed to the right, including deletions. If you don't want anything deleted on the NAS when you delete from your PC, use Contribute instead of Echo. Contribute does the same left to right actions Echo does,
but it will not delete any existing files on the right.
Hope this helps.