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But what you want is to remove tags that are only used x times isn't it?
You could do it like this.
Sort on usage
Tell calibre to find books for any of the criteria
Select first tag.
ctrl + click on some more tags you want to remove.
Select a book
ctrl + A (selects all books)
E (Edits all books)
remove label: (put the labels you selected here)
You could also do this with all your books selected and have a look at your 'Top x' of minor used tags
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