Is there any harm is manually modifying file_managed status?
No there's no harm in modifying the table manually, as long as you know what you're doing.

If there are no references to the file in the file_usage table, and you don't need the file any more, it's perfectly safe to simply delete the line from the file_managed table. Alternatively you could set the status for that file to zero in the table, and let it be deleted automatically on Drupal's cron run.

The advantage of doing it that way is that the physical file is also deleted automatically so you don't have to clean up yourself.