I never changed the SG stuff I kept it all untranslated, which is why I was so confused about this. Thanks for the reply though.
Now I rechecked everything just to find out that I actually didn't break anything.
Using the save I kept using to test I can complete quests without the required items on a completely untouched Japanese original. So either some quests are broken in general or the save I used to test is.
That is 2 days I'll never get back.
Will now work on the DeepL remake (with translated quests too) but that is going to take a while. DeepL is seriously shitting the bed since a few days. Every second output is now this "I'm not sure how to do it, but I'm going to do it" error bullshit.