[Damo]

Yeah, sometimes the lights that point at the flag glitch, and most of the time they make the flag black, lol, go figure. That's why I use the flag mod, because it stops that happening.

I'm guessing then that the ship was already illuminated, although in your post you did say the ship's lights were 'darkened', hence the confusion. Well rule of thumb is that they are neutral, unless of course the country they're from turned hostile since the ship left port, as it will retain the lit textures despite turning hostile mid-trip.

A rare find, but possible.