When you repair a ship with a core on it, it doesn’t repair the original core back because it already has a core. That would be an exploit to have 2 cores. So when you repaired it, you then removed the only core it had. It’s probably been deleted by now for being a ship with no core.
The ship had 2 cores one green and one alien core. I removed the green core. A ship can have two core if u repair it to template and not place a new core over the old ones location.