Tried using the Clip > Audio Options > Breakout to Mono to separate the stereo track instead of the Modify > Audio Channels > Mono Track Format, and it’s not killing the audio for the merged clips after saving and restarting premiere. My guess is that Premiere was having trouble indexing the audio files after a restart using the latter method, but as the former names the new files separately and links them to the master clip it must be able to keep track of the data.
…or something.
Anyway, thanks again for your help. I’ve got me some resyncing to do.
-m