I am also experiencing this issue after an AMP update. The instances still exist but are considered unmanaged, trying to recreate an instance to SFTP the old datastore into the new directory results in this error.
Did a bit of digging, following the process here (AMP Instance Manager Not Working After Update - #2 by ThePotatoKing) allowed instances to be installed again, however the original ones are still not recovered. Backup the instances you already have as adding the new ones appears to be overwriting the original folders.