Well, I handled the problem.
Before, I exported using the Adobe Media Encoder and selected only the video for output.
This time, I manually removed the audio track and output it the usual way.
Four and a half hours’ worth of rendering later, it seems to have worked.
I still can’t explain why Encore saw those audio-less files as audio, but whatevah.
Now, five more hours for Act II!
Sigh.
Thank you in advance for any help you would have given me. 🙂