Damaged Upgrades still give benefits.
Slipstream Drive
Prelude: Once per turn, you may Catapult move either your Flagship alone or other ships from your Flagship.
Tractor Beam
When your Flagship is defending in battle, the attacker cannot collect raid dice.
Control Array
While your Flagship is in a gate, you may tax any citires in its cluster like they are Loyal. (Don't take Captives.)