I think I stumbled on a relatively easy way to solve my problem. I noticed that the subs were about 40 seconds late after the missing piece. Opening the srt file (I think that's what it is) that VobSub made when I configured the subs in Moviestacker, I read at the top of the of the file, above the timestamp information, that you can resync subs by inserting a gap. I did so, a minus 40 second one, and it seemed to do it. I viewed the result in TMPGEnc in the Source range viewer of Settings. Seems to be insync now.