So, I am new to modeling and texturing. I am building some starships using blender (using parts from Shipyard) and trying to texture them. I'm... learning.

I built the models by pasting together existing pieces, almost always using the mirror modifier in Blender.
Well, as I am trying to work with them in Substance Painter, I notice that wherever I have a part that is doubled, one of them is just fine, but the other seems see-through. Like, there are red ploygons, but they are transparent. I can't access its polygons. It looks normal in I-ray, though. But, if I try to texture it, it's like the textures show up on the inside, rather than the outside.
An example is this model I am working on (attached). The lower "warp engine" appears to have glow only on the inside. The walls are see through, whereas the ones on the top are solid. When I look at in in I-ray, the one on top looks right, but the one on bottom is just basic textures. Anything I have masked out to be emissive doesn't show. What am I doing wrong?