Kibbelz plans to make a test server where he can view what's causing this issue (test server is for many other reasons as well), I was hopping on AGD in hopes that someone had this same issue and it was an easy fix.
I just tested and it saved properly for my first batch of edits, then I rebooted to make changes again, rebooted and the changes were reversed.
The game I work on is Nightmare, it's pretty big at this point so I imagine there are many global variables being changed. I can't confirm this (because I'm mostly an artist) but I'm fairly certain that would be the case.
Do you think it's a good plan to try and recreate this issue with a fresh install? I can do that in a day or two to see if it's my PC having issues.