I can't believe that I *just* found this website! So, we are having the same issue - lots of home folders being deleted, quite randomly, by Windows 7. I have an active Tech Support case open with Microsoft and my Account Rep just moved it to a Premier Support Case because the lower-level techs haven't found a solution. The case has been open for nearly 4 weeks, so I believe it is either a bug in Windows 7 or some application is deleting the home folders. The deletion happens on login.
A few things have helped, like turning off IPv6.
I also created a workaround, which was a PowerShell script to prevent users from deleting their own folder by resetting their NTFS security ACL. That did work, but I later removed the workaround so that we could continue to try to pin down the problem - I didn't want a band-aid solution, particularly one that requires a custom script.
Additionally: we ARE using offline files (and I want to use that feature). We DO NOT have quotas.
I also manage this daily through a PowerShell script which compares home folders to AD student accounts. I run it every couple of hours and it tells me if folders were deleted, so I can restore them and move on. With Volume Shadow Copies turned on, it's easy to restore the files ... but we are also a small district.
I am running into this between 2-5 times per day at this point. It was 10-20x/day at he beginning, so some of the measures I've taken (mostly, turning off IPv6) have helped.
I also resolved the "My Documents" issue via a PowerShell script - by changing the security on desktop.ini so that Administrators don't have read-access to that file. At least then I can see the whole list of user folders by name from the server share. Another admin I know has a logout script which deletes the desktop.ini file at logout.
Wow, I am so happy to have found this forum with other school tech people! We have a great email list in New Hampshire, but it's comforting to see others in other parts of the world who are having the same issues.