Sounds like your users moved the shortcuts from one location to another and the restore put the emaiil back to the original location.
i.e if i archive an item in \inbox, but then move \inbox\mySubfolder
If i do a restore to the original location, such as through Export Archives Wizard, then it would go to \inbox and the shortcut would remain in \mySubFolder
If i do a restore through the EV Client i can get it to restore to \mySubFolder
In Enterprise Vault 8 there is the Update Shortcut Locations which would update the EV references to move the shortcut from \inbox to \mySubFolder
the restore should then move the items back to the new location as opposed to the original location, except for a known issue when restoring items through AE, which regardless will restore to the original location.
https://www.linkedin.com/in/alex-allen-turl-07370146