Does REX change aircraft lights? I guess it is possible but I have never seen anything about this before.
Yes, I learned this the hard way a few years ago when I first got REX. If that particular box in REX is checked, than it will overwrite the main texture file for the some of the lights (I believe the file is called "fx_2.bmp, and its in the ../effects/texture folder). I remember how much that really pissed me off. I hope r4y30n has texture backups.
Nope, no backup. Although with all the different kinds of airport lights they give you to choose from I feel like it should be a simple matter to whip up a non-blue tail light... Granted, this does not affect some other aircraft that use custom lights, like the VRS bird.