You're right. Every time you go back to the cosmodrome, it's the same way it was when you first got there.
What I really found annoying was the way Fallen ships slipped in the same two places over and over. They weren't even trying to do anything or work towards some goal. Their ships just comes in, drops off the same units as last time and you kill them... Again.
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I know they they dont die like most other things but it just starts to wear on you, then before you know it you have got the achievement for killing 500 of them and can barely recall a single fight worth remembering.