The proper fix for this issue is to define a special format called "MASTER" (which is just a zip file). Then whenever you do a format-format conversion, calibre will automatically put the original into the master. If you do a format to format again, calibre automatically uses the version from master (if it exists).
And of course there will be aright click menu to update the format in the master, in case you hand edit the file.
Unfortunately, this is rather a lot of work, and I am swamped working on the new database backend at the moment. So this is another item on my TODO list. Indeed, IIRC this was discussed a few months ago.
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