Perhaps an easier way if you have a Windows PC to hand.
Connect to PC in Storage mode, right click drive then select properties then tools & you get options to fix drive as well as defrag. I have used the defrag a couple of times.
Don't forget to set to Storage mode in PC link settings, does not need any PC sofware.
Mike
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With the drive connected to windows thu storage mode, one would need to use chkdsk, or open disk properties and "check for errors" (same as chkdsk).
The problem I had above was with misplaced clusters. Defrag won't fix these, but the above method using, (disk properties and "check for errors"), will.
Most of the time if a hard drive has lost clusters or cluster problems, A defrag program will complain, and direct you to "check your disk for errors" first.
I preferred to use the "Linux" method, because I wasn't sure what was wrong in the first place.