Just posting to say this isn’t dead. Still working. Couldn’t get the hang of any editors, so I’m going back to womble. Accidentally discovered that the problem with the pops at cut points doesn’t happen if I work with elementary streams as opposed to an already muxed file. Sortof a bummer, because before I had all the different sound mixes (some with the center channel muted to use for transitions without dialogue) I wanted synced up and muxed together so that I could switch between audio mixes at any time with zero effort and it would already be in the correct place for sync in the timeline. I may see if I could still do this with a dummy video track and just use an elementary stream for the video and see if that will still fix it. If not I’ll just go all elementary and it will just be more of a pain.