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If you want to remove a book format from Calibre, you should not do it directly at the OS level, but via the Edit Metadata options within Calibre which also support tidily removing a particular format. This ensures that the Calibre metadata database accurately represents the books stored on the underlying file system.
Having said that my recommendation would be to keep all formats if you can. Ebook files are small and there are times it is useful to have the original source still available.
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