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I don't think there is any particularly "graceful" way to handle this situation.
You could simply ZIP all of the files relevant to a particular title together. Perhaps adding a note in the Comments saying something like: This is not a standard ZIPped ebook, this is an archive of various media, in an assortment of file formats, which will need to be unzipped before use.
I suggest the comment because calibre itself will think it's a ZIPped ebook and, upon trying to open it, might report an error. Without the note you might no remember this is an archive instead of a book.
However, I know that some other users have found a way to use Symlinks (no idea what they are, just remember the term) to include/cross-reference other file types into calibre's database to a limited degree. I cannot advise you further as I don't have this issue with my library. Just wanted to let you know it might be a viable (and searchable!) option.
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