Thanks for looking into it. What I've found is that the effect itself isn't hardcoded. I've successfully changed that by adjusting the gs_shipphasedout file. Unfortunately, I can't seem to find where the game is telling ships to phase out once they enter into hyperspace (phase space ingame). That is what I'm afraid is the hardcoded part, in which case I need to get in touch with a developer.
The nearest thing I've been able to come up with is adjusting the Solar Cloaking buff to cancel out the PhasedOut modifer inbetween planets, but that didn't have any effect (not in the one or two methods I've tried to implement so far, anyway). At this point, any help is welcome.
