Is there any way to use a trainer editor on a ROM that has new scripting in place?

[quinn_today]

I'm making a FireRed ROMhack that adds new dialogue, scripting, map editing, and trainer battles. I got Hopeless Trainer Editor and on a clean, unedited FireRed ROM it works great, fantastic. However, with my other FireRed ROM that already has some new scripting and dialogue, when I open the .gba file HTP says "Unhandled exception has occurred in your application." At the bottom, it says the problem was "Index was outside the bounds of the array."
Now, I realize that I could just take a clean ROM, edit all the trainers I want, then open XSE and add the scripts I want, but that's not feasible because there's a high possibility that I'm going to need to edit some trainer battles along the way as I test things out.
I don't know a ton about coding, but I've been using XSE to add the dialogue and I think I might have been expanding the ROM slightly? So if that's the case, then I guess what I'm asking is, is there a way to edit the trainers on an expanded ROM?

 

[ShinyTillDawn]

Perhaps it was looking for data you may have unknowingly overwrote with XSE.

 

[quinn_today]

Hmm... That does sound plausible. Can you think of any way to get around that? So far I've written all my scripts past the 0x800000 range. It would be kind of a pain, but if there's important data located there, I could imagine rewriting all my scripts to be even further, like 0xF00000 or something. Do you think that would work?