Your "My Documents" folder should contain a "SH3" folder. This contains your gameplay settings (sound/language/display settings etc.) and, most importantly, your careers. After reinstalling SH3, all your careers should be intact. Just move/copy the folder you backed up back to its original location.
Of course, just like you should add/remove mods only when at port, there might be loading issues with games saved at sea unless your new install is identical (modwise) with the previous one.
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