Hi Matt, probably a little late but....
I sort of had the opposite, after adding a scale level with that tool I still had to go to the Service through Manager and adjust the Maximum Scale and restart the service in order for the Create Tiles to recognize the newly added scale. Maybe you have to do the same to make sure it know that your bottom scale was deleted. curious if you Max Scale is still your previous bottom level or if that was removed and it shows your new bottom level yet?
just a thought, haven't tested it.....
Dave
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