From personal experimentation, I've only had chapters / scenarios skipped when overwriting one save with a whole different save, and even then it's only happened twice during many different tweaks and changes I've been using the editor with for testing purposes.
By this what I mean is;
- I have a save that is all the way back near the beginning of the game, to be precise it's just before the first mission you take your students on to fight bandits. For me, this is in Save Slot 4, and it's file name is slot03.
- After making backups of all my saves, I proceeded to open a different save, one somewhere around Chapter 6/7 (I won't go into details about where it is in the chapter as that would be spoilerinos). This save was in Save Slot 2, file name of slot01.
- I edited the slot01 save using the editor, making minor changes to some characters and once again editing the number of Owl Feathers to make sure I had a definite way of knowing the changes were implemented, or at least that some where.
- Instead of choosing to write over file slot01, I wrote over file slot03.
This is where the nonsense occurred in which the entire first bandit fight had been skipped, but it has only happened twice so far and at different points in the story, leaving me unable to find out the specific reason.
As for editing specific items in the convoy, there is an entire Tab in the editor labelled Items, where the left-most part is your Convoy Inventory. You can edit any item in that section to have 99 of said item, so for Dark Seal you would just find the item in the Convoy Inventory and set the Amount to x99 - or if you want to add them to a new item slot in the Convoy, the item ID in the available list is 1157 for Dark Seal, so just find it on the list and set it manually.
I imagine something like "Convoy Inventory Items x99" is a relatively simple ask, however I'm not the one making the editor and I'm just using it to see the limits of what I can push the game to before I realize how little work I've actually done recently.