As KaleunMarco says, you will have to move the Silent Hunter install, otherwise Windows will roll back the changes the mod attempts to do, leaving you with a a mass of weirdness in the game. Refer to the Steam Knowledgebase Article
Moving a Steam Installation and Games for their methodology of doing the move. The way you do it depends upon if you have a usable 2nd hard drive or partition. You can run the game from a fast external hard drive, but it does have to be "fast". The definition of fast in this case depends upon your computer and the controller chip of the external drive...
Also, the other reason you might lose credit for a sinking (probably the one KaleunMarco couldn't remember) is if another Allied unit assists in the sinking, such as an airplane bombing the ship, or a BB lobbing some 12 or 16 inch rounds into it from the horizon. I have put five torps into an enemy ship, only to have an airplane "steal" the sinking credit (it was not registered to my boat) by dropping a bomb down the stack... oh well. The fog of war...
