Maybe this can be of use here "Map1 -Map2" in
C:\Program Files\Ubisoft\Silent Hunter 4 Wolves of the Pacific\Data\Terrain\Maps\Map2
its RAW files that controls the depth and stuff on the main map. Only a theory... i show you...
The light gray color is sort a shallow water, the darker is water, beige (not really visible here) is land.
More hints here
http://www.subsim.com/radioroom/showthread.php?t=111999
and here
http://www.subsim.com/radioroom/show...ghlight=format
These threads don't explain exactly how to do an atoll or a reef but if you try it out I think you might get the drift of things. I found this searching for something completely different. At least this will show up in game on the NavMap, if its actually there in 3D I never tested...but I guess it would be as the Map1-2 RAW sets the altitude of stuff...anyhow check it out it might be a lead.