XML files in mod folder not overwriting original XML

I'm trying to make a mod that changes examinations. When I change the values in the original Examinations.xml (no mod just editing the orginal file), the changes I want work perfectly when I load the game. When I try to make this into a mod I fail terribly. I followed the documentation tutorial step by step and the game even recognizes that I have a mod registered in the main menu. However, for some reason the edited Examinations.XML that I have in my mod folder doesn't overwrite the original Examinations.XML in the main database. When I load the game, every single examination (except Interview) is grayed out and the doctors can't carry out any of the exams. When I scroll over the grayed out exams it says "missing equipment" and "missing doctor" even though that's clearly not the case.

Again, when I edit the original XML file in the main database, everything works fine. When I try to keep the original xml unchanged and add a mod folder, the changes are not going through. What am I doing wrong?

Could it be because Examinations.XML is in the "Procedures" sub folder?