Have a generic object maybe even an invisible one, follow the ship around. Do this by using set_relative_position constantly. Then, when the ship no longer exists the object will stop moving. Create the anomaly on top of the generic object and destroy the generic object.
You could even make the generic object look like an anomaly, with bits poking out of the ship's hull. You could even name it "Anomaly."
Of course once you've got that you don't even need the anomaly. When the players get close destroy the object and give them energy (or torpedoes, or whatever).
"Damn the torpedoes! Four bells, Captain Drayton!"
(Likely actual words of Admiral David Farragut, USN, at the battle of Mobile Bay. Four bells was the signal for the engine room to make full steam ahead).