I wish I knew how it got into this state but I can't remember the events other than that at some point a huge number of folders that should have been in the Calibre Library appeared on the desktop (I'm using Win 10) and that's when I came to this forum asking for help.
In answer to the ducks question, no I'm not messing around any more, just following orders. And as far as I know the check didn't flag extra formats, but it's possible I missed that.
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