I think you are misunderstanding how Calibre2opds works.
If you are using Calibre2opds then it works directly against your Calibre library with the Calibre generated folder and filenames - not against an exported copy that "Save to Disk" generates. You will find that within the Calibre library Calibre will have stored the book only under one of the multiple authors.
I have given a more detailed answer with some possible ways forward to achieve what you seem to want in the
calibre2opds forum on getsatifaction.