Copying the game the way you did should work fine, but what folder are the various "Silent Hunter 4..." folders inside of? Did you make a "Games" folder and do what you did, or are you inside of the install default of C:\Program Files (x86)... folder?
Also, each of the modded games, as well as the stock game want to use a Save folder of "C:\Users \UserName \Documents \SH4, which causes trouble, since most of the game runs off of that Save folder data. That data between Stock and FotRSU can be quite substantial, and cause trouble for both versions of the game. You need to delete that Save folder game, then use the MultiSH4v1.5 applet in the FotRSU modded game's root folder, and create a new 3-character name for the FotRSU game, such as "FRS", or whatever you like. Then copy MultiSH4 to the "german" folder, and do the same, naming the new Save folder something like "Ger" or something. Leave the SH4 folder for the stock game then. Next time you start the game, it will create the appropriate data structure in each of those separate Save folders, and you should no longer have a corruption issue.
Next up is: did you use either the 4Gig Patch, or the Large Address Aware applet to set the FotRSU's SH4.exe header bits that show the game can do flat addressing? Look in the FotRSU mod's Support folder for the pdf "help" files in there for these and many more questions you might have.
