I have a feeling that you are making this much more complicated as I intend.
Lets say, you have a book in AZW3 format, because you bought it from Amazon. However, you have a Kobo reader, which reads EPUB. So, you convert from AZW3 to EPUB, and upload the book.
If you have two ereaders, one Kobo and one Sony, but want different conversions for the same book, you would need two EPUB formats. Therefore, you would convert from AZW3 to Kobo_EPUB, and from AZW3 to Sony_EPUB.
This has to be possible; probably even by changing the output plugins so they save the format as <name>_EPUB (or <name>_whatever) instead of just EPUB. In that case, there would probably not be a difference in saving everything as it is now; it would just be another format; just like AZW3, MOBI, EPUB... you'd have <name>_<format>.
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Originally Posted by Sabardeyn
Lastly, and I'm not sure I read this part right, but if you're getting rid of the original file, you can never reconvert.
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I do not rely on Calibre to store my original files. I store them seperately. If I ever need to reconvert, I'll remove all formats from a book, and drop in the original files. Worst case, I re-import the file as a new book.
At this time, my base format is EPUB, and my reader's format is AZW3, so there is no conflict. I can embed the font I want, and convert. If I get another reader, I would just delete all AZW3 files.
I don't like "ORIGINAL_EPUB" (or any other such files) as the solution. IMHO it should be possible to designate a format that should NEVER be touched. (Possibly, use "Default input format" for this). If you then convert an EPUB to EPUB, the original (very first) EPUB should stay as it is, and the conversion would be called <name>_EPUB.