Thanks for the answers! Just so I'm clear - I should not respond to the occasional invasions that happen now, until I see some capture missions popping up? I guess I can live with losing the odd facility or territory, if that's what it takes.
Is there a time limit to this? Do I have to get to 100% terraforming by a certain date?
UPDATE: Yup, you were exactly right - I sacrificed a couple of territories and waited until capture missions came up. I guess I was a bit too fixated on never losing a territory
I'm happily upgrading terraforming stations now, and hoping I don't run out of time!