After the update to Advanced Threat Protection 3.1, there is a data migration job that runs in the background. If you try to restore a database backup during this time, you will be shown an error that it cannot be restored and you will not be returned to the command prompt until the migration is completed in the background.
The SSH session can safely be closed. The ATP 3.1 software will allow you to perform the restore after the migration is complete. If receive an error after the migration is complete, first restart the ATP appliance. If you still see a restore error, please contact Symantec Technical Support for further troubleshooting.