Hopefully you don't have to re-install but if you do I have done the following:
Install SH3 to 1.4b then before doing anything else copy the whole SilentHunterIII folder to a blank DVD, then if there is ever a problem & your install is stuffed you only have to delete it & then copy back from the DVD, then enable your mods again including SH3 commander if used.

Also having a copy of stock files does come in handy at times.

Cheers.