Hi
First off, you have a conflict between mods. I don't know which mod does the flags but I don't think that was a stock feature. So, remove your mods one by one but keep your print of what ones you had and the order. (for later)
After each remove, run a single mission and see if the conflicts are gone. That will let you isolate which one caused it. If using JGSME mod enabler you get a warning when a file will get overwritten by another mod. Don't let it put that mod in.
When you find the problem mod, remove it, then load the rest of the list in the order of your list, one by one. Test each load in a single mission. Note any new problems or error messages.
You can also read the readme files for the mods to see which ones have mentioned flags or other "must have" features.
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