Uprading ship design (hull relatad)

[Kellicus]

"Well, maybe those stellar manipulation components are "destroyed" simply because they blow a bunch of fuses when used"

Perhaps, like the modern military, these components are replaced with "war ready" replacements.
I work on military fighters, and when we have a 'destroyed component' we simply replace it so the aircraft can return to service and then repair the damaged components when we have the time and materials.