If you have my Update as you say, use a newer build as specified on the 1st post of the Topic/Thread of the Update.
This is cause due to a new IFF feature, where all the $Team: xxxxx (ex: Friendly/Hostile/Neutral/Unknown) were erased if you saved the Mission with a FRED2 build around those dates...also this was caused if the Flag "All Team at Wars" at Mission Specs was ON, however in the last version of my update this happens only at Mission 06 (the blockade against the Kismat and the Diablo), I can't really tell if that option was activated by mistake by me or if it was already in the INF + SCP Patch missions...
I have already fixed those bugs months ago, but I still don't have upload the fixed update...