We have faced another issue during our migration to Exchange 2010, We had a situation where we had to move back some users to Exchange 2007.
Some of these users got quota full issue, they had deleted n number of items but still quota full message was hanging on.
Ultimately we used mfcmapi & removed the items from Recoverable items\ deletions folder which had done the trick.
So here is the concept behind it.
In exchange 2007:
When items are deleted from deleted items a deleted flag is marked & items gets hidden from mailbox but recoverable via recover deleted items.
Note :- Recover deleted items doesn't count for the Quota.
Also, this behavior is on per folder basis.
Recover deleted items gets emptied based on the retention mentioned.
In Exchange 2010:
When item is deleted from deleted items it is moved to Recoverable items\ deletions folder (hidden from users, you can see it via mfcmapi)
Recoverable items\ deletions items gets emptied based on the retention mentioned.
Behavior is changed and every mailbox has a single storage for recover deletions & it’s not on per folder basis/ flagged.
As the mailbox had been migrated to Exchange 2010, it takes the behavior corresponding to 2010 but when it is moved back again to 2007 it should resort to old behavior but this was not happening in some cases & Exchange 2007 is not aware about this folder so it counts it in quota.