I'm trying to do the same thing with a fresh install of SH3. I'm going from an early version of GWX to a different expansion mod. So I'm not sure if this is going to work as I haven't tried it yet.... I'm still working up the nerve.
I saved the SH3 folder in My Documents to copy back into the new SH3 folder created with the new SilentHunterIII install. Also copied everything in the SH3 Commander file in Program Files. All this was on my E: Drive to be copied into the SH3 Commander install on my C: Drive. Copy and paste so you don't lose anything you've saved and are moving. If you lose it there's no way to get it back again, unless you make a backup of the files you're moving about.
Sailor Steve says the ini. dll in SH3 Commander is needed to get it all to work. I wasn't sure which dll was the ini. dll, so that's the reason I copied everything.
Write down everything you do to get it all working. That way you'll remember it all if you need to do it again. And... you can let the rest of us know just how you did it if you're successful.
Good luck.