Auto-purges are unfriendly. Let the user delete it if needed, with the assumption that it only matters once the new.FMT is manually edited -- in which case the user can make an informed decision.
If not, how should calibre know that you are ready to sign off on the new.FMT?
Conversions are by nature lossy -- so unless the user confirms a new canonical copy, why convert from the intermediate format?
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