So it looks like it skips the part where it's supposed to add the input file.

subprocess.CalledProcessError: Command '['ffmpeg', '-v', 'quiet', '-stats', '-activation_bytes', '########', '-c', 'copy', '/dir/to/saved/file.m4b']' returned non-zero exit status 1.

I'm sure there is a better way to do this (I know just enough programing to be dangerous) but I made a patch file skip_rebuild.patch which should highlight the issue location.

After making the change everything seems to work.