A Dtrace of the ArchiveTask process will show that the IPM.Note.EnterpriseVault* message class items are being excluded (EXC) from processing. This will cause the task to not process moved shortcuts for IPM.Note items.
CMessageClassPolicy::PopulateFromExchangePolicyEntryId - Read MessageClass [IPM.Note.EnterpriseVault*] [2468146A368AA75489844DA35AA1D01941012700xxxxxxxx.xxxxx] [EXC] [Exchange]
This message class is not a default message class and would have to be added manually. The issue is that the message class has been added and is unchecked within the Exchange Mailbox policy.
There are two options to resolve the issue.
1. Ensure the message class is checked for processing on the Message Class tab of the Exchange Mailbox policy for the user.
2. Remove the IPM.Note.EnterpriseVault* message class from the site.
The next archiving run should now process the shortcuts and update their location properly.