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.