I had a similar experience where it deleted everything but the cmp from my bundle.
Kate, I checked the Pending changes and it had nothing under the Working Set or Other metadata.
Once re-created the files and put back all the code, TWS only updated one of the files. I had to quit TWS and re-open to get all the files updated.
At this point, I'm very wary of continuing to use this new version. Is there a way my colleagues who have not yet installed it can opt out of the upgrade until things are settled?