Go to the archives tab and move the main file you use for archive invalidation to the top, if its grayed out go into the settings menu, under the workarounds section un-tick the option "Force-enable game files" click ok then close Mod Organizer, when you reopen it the file will be movable.
the next step is mainly for those who don't use MO's automatic invalidation feature but id doesn't hurt to check that the ini file matches the AI file
in the following example ill be using Fallout - AI!.bsa as my AI file
go into the ini editor and use crtl+f to find the archive section;
find the line
SArchiveList=
it may look like this
SArchiveList=Fallout - Misc.bsa
here type the name of the archive invalidation file you use before Fallout - Misc.bsa
it should look something like this
SArchiveList=Fallout - AI!.bsa, Fallout - Misc.bsa
