Hi Psymon,
Yes, I edited my response as I did not see you had already posted. You want to add the audio file and make any changes you want on the epub2 side of things and *THEN* run epub3-itizer.
On the good news front, this bug does not exist in Sigil master (Sigil-0.9.4) as we have already reworked the complete Metadata gui editor and in doing that prevent the bug. I did try your test case on it and it passes with flying colours even if I add the audio file later. So all should work much better in Sigil-0.9.4 which should be out in under two weeks (barring bugs).
Thanks so much for the bug report!
KevinH
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