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excellent work Rongel  Now as I don't fully understand these occlusion and normal maps purposes, can you explain? Also can you tell us what you changed to get Zedi's ship fixed? I've noticed that many of the ship's from SH4 have an occlusion map (the _Oxx files) whose alpha channel doesn't match the RGB channels. Any thoughts as to why 
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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.