Wow congratulations on your release. It's amazing the dedication you and your team have to see the mod through after all these years. I just started a game and did the introduction and am already hooked. I picked the non-canon version of the story since I am a huge fan of the Jedi Exile and do not like what the novel did to them. I just have one minor complaint since the dialogue is not voiced the onscreen text moves too fast sometimes and I am not a fast reader. But no big deal I had the same problem in the vanilla game with some of the alien's dialogue.
Only global changes belong in the Override folder. Module scripts get injected into the appropriate MOD file in the Modules folder.
Can you attach a save file? The problem I had last time was that I couldn't reproduce the issue, so I was never entirely certain of the root cause.