I'm sorry for the delay in getting back to you... been busy. You've definitely probably hit on the problem with the Parts. I've never really dealt with Parts before. The only one I have is Mel Brooks' History of the World, Part 1 which was a movie. Many years later he came out with History of the World, Part 2 which was a limited Hulu series. So, they never interacted with one another. Have you ever thought of just combining the two parts into one movie, or redownloading the full movie and replacing that for the parts? I'm sure they are only parts because they couldn't fit on a DVD or CD as the full movie. You're not dealing with optical disks anymore, these are digital files and can be as big as you want. Besides, you can most definitely get better quality now as a full file than anything that had to fit on DVDs/CDs in parts back when you got them.
Otherwise, maybe Mark, the author of TVRename, could give some hints on how 'Parts' work within TVR. Or, maybe someone else.