Hi, sorry for the month long necro but I'm having the same problem. I am getting multiple necron terror missions every day, which I can deal with but it's just turned into a boring slog. Looking in the save file I can see that 53/67 bases are necrons.
I attempted to delete a bunch of the necron bases and get them down to a single base, but doing so corrupts my save file due to unknown UFO missions. I have tried deleting each related UFO and mission, but have not had any luck. If you know how to delete them without corrupting the save file, or by some other method, it would be a huge help