This problem should be fixed now. I was having the same problem so it was easy to track down. when a VM is deleted now, it should stay deleted.

For those interested, it was a little bug in the VM redundancy system that was triggered by the migration. We replicate VM messages so that nothing is lost in the event of a server crash, etc. You should all be happy that it worked so well

All humor aside, if this is happening to anyone after deleting a VM message as of right now, We'd really like to know about it. I've deleted a couple of mine over the past couple of hours and they've stayed gone. So it seems to be fixed.