How do you clear orders for population transfer? I don't have any installation orders, if that is what you were referring to.

Also, I can't abandon. As I said, I have an espionage team down there. They require a "colony", and thus when they were placed, it created one.

It may be a mute point here shortly anyway. My main fleet has finished its refit. We're off to war again. That world is the primary target.

This is late, but to clear the orders for the civilian colony ships, open the Shipping Lines screen (Ctrl + L), then click the colony ships in question and press the 'Clear Orders' button.  The colonists they are carrying vanish into the ether and they return to the nearest trade center.  You can SM the lost colonists back onto their source body if you want.

Nope, it's the same way when you use genetic manipulation to make new subspecies. Each species/race gets its own colony, and no there's no simple way to move installations from one to the other overground

Remove the espionage team using the teams/academy tab of the population and production menu, abandon the colony, then just use spacemaster to put an additional 250,000 pop on whatever godforsaken rock the lousy colonists came from in the first place. Then if you really want to repair all the damage use spacemaster to increase your wealth enough to subsidize the shipping companies for their losses.
Roleplay that their insurance has come in.

When I get home I will look for it. For some reason they frown on installing stuff like Aurora on work computers

As an addendum, civilians will tend to avoid systems where gunfire has taken place. The cooling off period is usually around a year for the "fear factor" to decay low enough to make the civs go in again.

The thing I am thinking of is the danger factor. Systems where ships get blown up, hostile aliens, warfare, etc increase the danger factor and the civs avoid it. You could also use the ban body on the single planet in question and they should respect that. Especially if there is 4000 missiles floating about.

I'm not seeing it :/ Ban Body is in F9's display, but I don't see a system wide forbid.

How do you clear orders for population transfer? I don't have any installation orders, if that is what you were referring to.

Also, I can't abandon. As I said, I have an espionage team down there. They require a "colony", and thus when they were placed, it created one.

It may be a mute point here shortly anyway. My main fleet has finished its refit. We're off to war again. That world is the primary target.

Is there a way I can stop them from this?

I have a populated colony that is actually the homeworld of a hostile race. The fact is, the planet was SO good that the civilians just immediately started traveling to it with colonists (it's Earth-like, 0 colony cost). The world now has about 250k people on it, and each time they bring another colony ship... it's destroyed by defenses. Only after they've dropped off their people, of course. So, it keeps growing, and the companies are losing money.

I could abandon the colony, but that would result in the death of 250k people AND my espionage team.

Ban body gives me an error saying that it can't be used on a populated colony.