I have bulit very different EAW worlds for twenty years, so I have huge experience of mismatched missions files, right from when I built the Midway theatre in 2000. My experience was that If you have a theatre mismatch - down to changing position and alliegience of bases - you will get a CTD before you get to the hangar screen.

But this problem is sorted now because each scenario has its own gamedata folder for its own mission files.

Then you would avoid a CTD after the hangar screen - caused by planes mismatch - by not flying any default "last mission" if you have installed a new planeset.