I recently worked a case that was a little fun.
In this case, the tenant was in a hybrid scenario with Exchange 2010 on prem. When he was attempting to move a few mailboxes back to on prem he was getting the following error:
Error: MigrationPermanentException: You shouldn't migrate mailbox 'John Doe' to Exchange 2010 or an earlier version while the user's Instant Messaging contact list is stored in Exchange. If you do, the user could permanently lose access to their Instant Messaging contact list, which will cause serious data loss. The Exchange copy might be the only copy of this user's contact list. To continue, please contact your Instant Messaging administrator and make sure that the user's contact list is moved back to the Instant Messaging server. After this has been done, you should be able to complete this migration. If you must migrate the mailbox despite the potential data loss, you can do so by running 'Set-UMMailbox mailboxID -ImListMigrationCompleted $false'.
The cause of receiving this message is that at some point, the user logged in using the Lync 2013 client. Once this is done and the mailbox is on Exchange 2013, a feature called Unified Contacts Store is enabled. This removes the user's Lync contacts from the Lync database and places them into Outlook. In order for this to happen, three conditions have to be met.
1) User must have a mailbox on an Exchange 2013 server
2) User must be on a Lync 2013 server
3) User must log in with the Lync 2013 client.
The real problem came when the administrator tried to run the Set-UMMailbox command referenced in the error, and got a new error stating the referenced mailbox was not UM enabled. This could be resolved by changing the 0365 license assigned to the user, however in this case the tenant did not have any of the appropriate license available. Fortunately, this situation has been repaired in a way. The switches referenced in the error now work with the Set-Mailbox command, so the proper command would be:
Set-Mailbox mailboxID -IMListMigrationCompleted $false.
Hope this helps anyone that feels stuck with this error.