I've 'struggled' with this issue since I started using calibre a couple of years ago, and there have been many threads created seeking solutions. Two methods have or are working for me.
- Put them in an archive that Calibre wont process. Add the archive to the book and put a note in Comments - eg "The xxx archive contains the following additional formats...". Calibre will keep track of the archive through renames, library rebuilds etc. All you'll be able to to with is to open it with your unarchiver. From there you could drag a format into a 'scratch library' (via the file system) for additional calibre processing.
- Or keep them in a folder outside the library and insert a link to the folder into Comments labelled "Other formats are Here". With a list of what's there
I now use the second method in preference to the archive method - I keep the additional formats in my CalibreLibraries directory within a directory structure that mirrors the library structure :-
Most of my books don't have 'supplementary files' which results in a sparse mirror, I can't say that this approach would work (procedurally) if that was reversed, I'd have to suck it and see. Off the top of my head if most of my books had 'supplementary files' then I'd probably use the archive 'solution'.
The most common reasons for me having two files of the same format for the same book are different editions (e.g. draft and final) and different languages. Also multiple film and TV mini-series productions, IIRC the BBC alone has done at least 3 Madam Bovary's and there are maybe a dozen films...
BR