Very nice Qaanol I never thought about using the undestroy command.

That's a good explanation, Qaanol. Thanks. But I guess I'll have to make the new alternate systems to include the new hypergates... I'll just have to stick to non-mission systems then.

You could put them in a seperate government for each pair, and then put all of the governments in one class.
EG:

spob 128 and its replacement spob 129 are in govt 128

syt 128 with spob 129 is in govt 128
syst 129 with spob 129 is also in 128

spob 130 and its replacement spob 131 are in 129

non-replaced spobs are in govt 130

govt 128 and govt 129 are both in class 1 and one of them has 1 in the allies field.

This means by selecting 'any spob/syst in a govt' you can allow spob/syst specific missions
(10,000 + govt id)

By choosing 'any spob of this govt or its allies' you can allow 'govt' specific missions.
(30,000)

Hope that made sense. You'll get alot of govts this way but it does solve the problem.