I had to reset the Navigator metadata server and followed the steps below:
1) Stop Navigator Metadata Server from CM
2) Take a back up of Navigator Metadata Server Storage Dir (if you want to archive the old data)
3) mv <storage_dir> < new_location>
4) Back up your navms database
5) In NMS database run:
"DELETE FROM NAV_UPGRADE_ORDINAL;" "INSERT INTO NAV_UPGRADE_ORDINAL VALUES (-1, -1);"
6) Start Navigator Metadata Server
this will delete all metadata, custom data added in the Navigator UI but does not affect the Audit logs visible under Navigator UI -> Audits.