My fallout.ini keeps resetting to vanilla when i start nvse through MO2 even though i set the file to read only, but my FalloutPrefs.ini stays the same.

Might sound obvious, but did you use administrator rights when you set the files to read only? Same for MO 2? I always do when it comes to file settings and as a user of MO 2, I don't recall that happening when I use the administrator settings.

@"jacoboriley" I've tried to set the file to read only with administrator rights but it causes MO2 not to start because it can't archive invalidate. I've tried just simply clicking the read only box but that doesn't work either. This just start happening after i updated my computer from windows 10 1709 to 1803.

Might want to head over to the MO 2 discord server and see what they have to say unless someone here with more experience than myself has an answer. MO 2 did just update. I'm using both the update and the current version of Windows 10 without experiencing the problem you are having....which sadly doesn't help you.

@"jacoboriley" Was about to shoot my computer till i found this post https://github.com/Modorganizer2/modorganizer/issues/477

Rpkiller1 wrote:

@"jacoboriley" Was about to shoot my computer till i found this post https://github.com/Modorganizer2/modorganizer/issues/477

I didn't even think about the "install MO 2 outside your game folder" thing along with any tools run from MO 2. I've been using it and installing it outside my game folder for so long it's become second nature. +rep for finding that link and sharing. This fixed your problem I hope?

@"jacoboriley" Seems to have worked i reinstalled the game then replaced the ini