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It can be for a number of reasons. The White Star was moving
through a highly charged atmosphere, which would leave detectable
trails; it was being fired at by the shadow vessel, which would've
attracted considerable attention from the flares; diving at that speed
and coming back up there would be considerble heat on the surface of
the ship (not normally a problem in space); and it was pretty much
shaken up/partially damaged during the fight. Also, at that range,
once you're near enough, you can pick it up visually as it gets close;
it's not a cloaking system, only a stealth system.

jms