Our district recently migrated 1600 users from a legacy Exchange server to Exchange 2013 SP1. The general users only had 5MB as the send / receive quota. During the migration, we noticed that the users who were at or exceeded the quota lost their Inbox, Deleted Items, Sent Items. However, they were able to locate and recover them from the Recover Deleted Items folder.
The Exchange 2013 databases offer them considerably more space and their limits have been increased to a 100MB quota. We can restore the missing items from Recover Deleted Items. However, at various times throughout the day, those same user's folders continue to delete, without any user intervention. They recover them again, only to see the server delete them again, despite the fact that they have enough storage.
There is nothing to discern in any of the event logs about what is causing this. The times of the deletion seem to consistent as well, 8:30, 1:00, and 3:30pm. We have found the only way to correct this is to restore the deleted items, move them to a PST, disable the e-mail account, recreate it, and then restore contents from the PST.
This is affecting a couple hundred users and we cannot find any suggestions.