In case anyone is interested, here is the response I got:
"I'm sorry for the problems you experienced with this. I spoke with
one of our admins and he believes this is because we were in the process of offloading a bunch of users accounts to a new faster file server at around the time you wrote in. We were doing this to help prevent any one file server from being overloaded. It's possible that the files that were reverted were a result of the initial copy completing and the final rsync running. I checked in your directories and saw that files were uploaded shortly after you wrote in, so it doesn't look like this has happened again. I don't think you should have any further issues with this, as all of your data has been moved. If you do experience these issues again though, please don't hesitate to let us know."
Still not happy that two hours of data is gone for good.