Correct. Consider the big picture here: if the MPLS #'s are missing, then any episode mappings are corrupt and worthless. So you have to delete the discs, re-add them, use the original discs to grab the title/chapter index, then lastly map each episode on that disc.
I also want to caution you here: you keep trying to take the shortcut back to loading the episode mappings from the online My Movies repository, and you're making a huge assumption that those mappings are correct. In my experience, they are only correct about 10% of the time. Often they are missing, or if they are there then whoever did the mapping got them wrong. I ALWAYS double-check all episode mappings with each disc I add, and I ALWAYS assume the My Movies data contributed by other users is wrong.
I and a few other users have made a feature request to Binnerup to make some much needed improvements to the episode mapping panel. Basically, we've asked for filters and sorting so that we can easily find the handful of episodes hidden amongst sometimes hundreds of titles/chapters. Brian said he would work on it, but so far nothing...
Just because episodes appear mapped doesn't mean they are mapped correctly. Sometimes the user who get did the mapping gets the episodes mixed up with each other.
As a newbie I understand how intimidating and daunting this task seems to you. I was in your shoes a couple years ago. But now that I've got the hang of it, I can typically map episodes in about 2 minutes per disc.