When you make changes to the terrain a file is created in *:\Ubisoft\Silent Hunter 5\data\Terrain\Data\DetailMasks
Typically a couple of raw files and a dds
You will need to add the file(s) to your mod
I have one install for modding and a back up install - and used winmerge to tell me what was new in the modded install so I could copy that into the mod itself
I have added some ports on the resupply mod and changed terrain around those and El Ferrol which you couldnt get into
The game has produced 16 raw files and 4 dds for that in the DetailMasks
Hope that helps
EDIT
The mask asround ports do overlap as each port 2d contains some land
Zoom into Cadiz and take a look at that
Not very helpfull those port masks