Well, obviously some deleted files resurected after your uvs2 sync...
I have just checked loading full update block into fresh empty dirs and nothing like that has happened for me. Could I ask you for compiling fresh uvs2 from current uvs2 tree (or snapshot) and repeat Sync? (in hope that it was just some gone uvs2 development anomaly..)
BTW, there is also a uvs2 functionality to revert to (or resurrect) older file, but I do not think that it is what you have done...