Chapters simply have names, and the tool wouldn't know that its supposed to increment some number in some string, so you will have to fix that manually.
For the cutting, the way i did it was in two steps, first mux the two parts and split off the parts i didn't want anymore (you can pass frame numbers if you want, for splitting from the start thats fine, from the end finding the right frame number is a bit harder), and then the two perfect parts without any extra content i merged. This is destructive and obviously deletes the parts you didnt want anymore.
You could also merge them without removing the parts, and then use ordered chapters to skip them, but it'll require manually crafting the ordered chapter layout, which may require some more time.