There is no "upgrade" for the SDK (you'll get in lots of troubles as you see now)
The most problematic part are the links to already isntalled shared objects (they can't be used twice and will end up in error messages while installing and a not 100% functional SDK)
Believe me, i did it wrong myself
1) Install the SDK to a NEW directory
2) Reboot
3) Delete the old SDK directory
4) Let AmiUpdate find and install all the updates
5) Happy coding
Edit: Don't mess with the SDK afterwards (paths, assigns etc.)...it's in a state now that, if installed correctly, works perfectly fine.
Again, believe me, i did it wrong already