Your career is saved in your My Documents folder in XP in a folder named SH4, similar location in Vista where its called Documents instead of My Documents. Normally, uninstalling your game won't delete your saved games without asking you first, but its not a bad idea to make a backup copy of it 'just in case'.
Check your realism settings, I can't remember 100% if they save as well, I think they do tho.
You may want to make a note of what mods you have enabled before you uninstall, and in what order. There is a better than even chance your savegame won't work again unless you reapply these mods, particularly if you are using any supermods. Disable all your mods before uninstalling the game.
You might also want to return to port before uninstalling, just to be on the safe side.
Before reinstalling, it may be a good idea to delete the "Silent Hunter 4 Wolves of the Pacific" directory (usually installed in Program Files), just to get rid of any residual files. You can copy JSGME.exe and your MODS folder out before deleting, and copy them back in after reinstalling.
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