@JohnL - Preferences->Add books includes settings for what to do with duplicates, IIRC one of them is to overwrite existing format
If you Remove a book with the Del key then the book folder and contents are removed. If, after a book delete, an author folder has no book folders then the author folder is deleted. You can delete individual formats with Alt/Del.
If you're not seeing an 'Are you sure' style warning messages then you must have turned it off, they can be restored via Preferences->Behaviour->Reset all disabled confirmation dialogues
BR
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