W/O going to far OT, if the resolution was left as is, isn't the only problem/concern is at the 'merge' (joint) point? As in a glitch just like mismatched video edits starting in the 80's using 3/4 U-Matic had well known 'edit' problems.
Interesting point about merging vob's first. I didn't think of that angle. But, coming from the same movie
Lastly, what's wrong with Handbrake?? Yours is the first really negative report of that program that I have read. You are saying that Handbrake caused the problem?