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Originally Posted by Rongel
Explaining what i did might be even more complicated than fixing it! Let's try... The occlusion map and it's alpha channel are indeed totally different looking, but it's not a corrupt or anything like it. So it seems we must leave it alone. There was nothing wrong with the two textures that Zedi sent me, the base texture, and the normal map. I used in this ship a dat-file that I downloaded here earlier and I could see it's occlusion map's alpha channel was different than in SH 4, it was edited. I just changed it back. Still, it didn't change in the game or in S3 editor. It seemed that the game sniffed the old dds files I had in the ships folder, so I simply deleted them, so that it must use the embedded files.
One weird thing I noticed is that the spotlight and guns cast shadows. I tried to use the shcontroller "VisibleUnderWater" to the whole ship and it vanished from the game. You could see it only underwater. Weird thing was that now the spotlight and the gun were rendered and had textures!
Okay one issue more. We can see water reflections in the ships structure near the water (when we aren't underwater). But why only in one side??? Stock ships have this effect on both sides. 
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Can you send me the files you speak about above regarding the occlusion maps? I'd like to see what you're talking about.
The spotlight and guns will cast shadows because they are being pulled from a gr2 file (they are SH5 guns and spotlight). Only items taken from GR2 files will cast shadows

This is that whole granny thing which is a total PITA!!
Now the likely reason why when the ship 'vanished' and all of a sudden the guns and spotlight rendered is because there are two ways the game engine can render items: the granny way and the old way. It can't do both on one object. Since we asked the game engine to render the ship using .dat files (the old way) it rendered everything that way, including the gr2 stuff. Now since the old way couldn't read the textures from the gr2 file (

) they show up as dark. This is my hypothesis.
Can you show a screenshot of these water reflections you speak about? I want to ensure what you're conveying and my understanding of what you're conveying are the same.