Without warning, synchronize has deleted my "My computer" folder. Including 10 GB of mp3's.
1. There are drives in "My computer" folder. They cannot be deleted.
2. Considering that you mean that contents of your drives were deleted (while you cannot obviously delete everyting, like Windows itself), yes it may be intended functionality, depending on what were the options for synchronisation. If you have selected local synchronisation (including obsolete file deletion) of whole local drive against empty remote directory, then you've asked WinSCP to delete whole your local drive.
3. How "without warning"? If you have clicked "synchronize" instead of "refresh" you should see with dialog for synchronisaton options first.