I went with a completely different approach: have every colony produce only robots (mainly for their own use) while the flagship produce almost exclusively ships.
My logic behind this was that the only resource you cannot afford to lose is your ships. You can rebuild colonies, search for resources, etc with a ship... But if you have no ships and no ship production capacity, you're done for.
So my colonies were pretty much self sufficient, and if the shit had to hit the fan I simply evacuated everything to the main ship. Starting with robots. I know this might sound weird to say, but the colons reproduce free and faster than what you can build robots. xD
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