Supposedly Figured it out
So it would appear that in SP1, Microsoft introduced EWSFindCountLimit throttling. It will search for the first thousand entries, maybe on one user, or across all users, then respond to all subsequent find requests with an item not found message, which causes BES to think that the item has been deleted, and it tells the device to delete them. It will be fixed in SP3, but there is a workaround:
Set the EWSFindCountLimit to $null
1. On a computer that hosts the Microsoft Exchange Management Shell, open the Microsoft Exchange Management Shell.
2. Type New-ThrottlingPolicy BESPolicy.
3. Type Set-ThrottlingPolicy BESPolicy -RCAMaxConcurrency $null -EWSFindCountLimit $null -EWSMaxConcurrency $null
4. Type Set-Mailbox "BESAdmin" -ThrottlingPolicy BESPolicy.
Good luck!
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