AHA! Finally found it! I'm not sure how I didn't see it before, but the step I was missing was to go into the MIDI editor, select all notes, right click, and then simply go to Note Channel and change it. Doing that and then doing a MIDI export does indeed appear to preserve channel data. Also of note, dr_midi.pl starts counting channels at 0, so it's output ended up matching what I was seeing (I assume channel 0 meant all channels, but it really meant the first channel, normally channel 1).
So I think my problem is solved! Thanks for the help everyone!
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