If Recover detects a problem, replace your file with an undamaged back up. You may have to save a clone of your file and import all your data from your recovered file, being careful to update any auto-entered serial number fields.
There's just no guarantee that your recovered file will work correctly, so it's safer to go to a back up copy.
Does the recovered file fix your problem ?
If so, you should definitely go to a backup of the file..
I also just wanted to add a note about the recovery message.
If the recovery shows "Structure: scanned ; XX item(s) modified" and no other issues, open the recover.log file and check to see what these modifications where.
Filemaker Recovery (in my opinion) is incorrectly reporting Rebuilt group with x object(s) as corruption, when it should be nothing more than a notice, it certainly should not be stating to 'not to use the file going forward'