I don't know if there is a way to add a blacklist mid mission, if there is that would probably be the easiest and someone will surely tell you here.

If it's not possible you could maybe accomplish the same thing this way (not tested):

• make several objective modules with the different blacklist markers you need for the missions. So you have one with the config for when side mission 1 is active and so on.
• Then sync each objective module to it's own unique version of a "Military AI Commander" module.
• By using triggers synced to the commanders you can choose which one should currently be active.

again, not sure if this even works but give it a try =) It may also be possible to use one commander instance and re-sync that one by script to the new objective module. but I have no clue how the communication between the modules are handled under the hood so that might not work.

@Imbazil: Thank you for the reply! We are trying to avoid explicitly black listing these areas from the editor so that they will still be dynamically occupied by opposing forces while not in use as venues for side missions. I like your idea, but it may be a bit onerous given the number and diverse types of side missions we are supporting at the moment. We have markers available for each side-mission's AO, we just need a way to reliably clear these areas of active forces.