barak, Gray Lensman has excellent advice! Think of the "SH4" folder as something you can get rid of as often as changing your socks. You'll need to re adjust your resolution (and a few other personal preferences) after deleting the SH4 folder, but getting rid of the older saved points will keep the game running smoothly with a new install. Never replay a saved point that doesn't have your current mod setup "activated" in-game. Saved game points must have the same mods installed as when they were saved.
What's important about your issue is to make sure you remove
all of your old installation, before reinstalling. Follow what's written
here for completely removing your old install.
You didn't post you computer OS or specifications, but the info about a Vista install should be followed for any newer OS. Even if you have a Steam version of the game. Personally, I think Steam is a crock providing the 1.3 version of Silent Hunter 4 as its "base" install, then offering version 1.5 (the U-Boats Add on) for an additional cost!!
If you have more than 2 gigs of memory (most computers have much more these days), install the
Large Address Aware app to have your game access more than its limit of 2 gigs. Works for most older games....I used it for Sid Meier's Railroads and prevented CTD's every time I played it. just follow the directions for installing it.
Speaking of installing, after a clean install, and adding JSGME to your game, don't forget to make a "Snapshot" of your clean game files before adding any mods to it. You'll use this "Snapshot" to compare your game files after adding/removing mods. JSGME put this feature into its app because it knows trouble pops up all the time with mods corrupting game files.....use it as the instructions state.