If I'm not mistaken, you could have just restarted a copy and been fine as well. Sync only makes the remote match the source. In other words it adds or deletes to make them match. Copy also checks what's there, then uploads what's missing, but won't delete. I personally only use copy, in my crontabs and stuff, then only manually run syncs when I know the local data is good and I want them.... Well.... Synced.
That way if I lose something local, and don't realize for awhile, I can recover it.