I am pretty sure it is how it works. The save keeps the ongoing missions under "AlienMissions", but also the possible missions under something like "AlienStrategy". I remember Meridian going through things to find which mission he had missed during the first two game months of his LP, basically crossing off the missions that were in saves both before and after (meaning they hadn't happened yet) and finding which had disappeared.
I am, of course, not saying that this is a reason not to add new missions or new races! I will happily attack and loot more varied targets
BUT, I am saying that, when you tweak alien missions, a word of warning might be nice, so that those of us who have an ongoing game and want to keep it updated can go into their saves and add the missions as missions which did not happen. I don't have much time to play and am only in.. June or July of my first year after 2 months of playing, so the option of finishing and restarting is not really one, and aborting is not so much fun since you end up playing the early game many times and never seeing much new stuff.
Also, oddly enough, infiltration missions are awesome in Piratez. Funding is very low any ways, so losing a country doesn't matter much. However, the shipping traffic (all of which land!) is incredible. You can make a LOT of instant money from looting, an amount that easily compensates for ~two years of funding lost from that country. Not really a question, but more of a comment/realisation.
Also, did you change missions so that the happen where you have bases? I have been VERY lucky otherwise, as I have had a regular (non-pogrom) mission spawned in my starting region every month so far. If yes, that's a very nice touch and makes it feel like the planet is more active.
