I must admit that where I have multiple formats of a book I simply keep all of them.
Calibre does the housekeeping so it is not much effort, and if I later find I need one of the other formats for any reaon they are then available.
As has been mentioned sometimes I find my prime format (EPUB) turns out to be badly formatted, and having the others available increases the chances of having one that is well formatted which I can then put through Calibre to create other formats.
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