BuddyPress.org

That makes things clearer. So this is what I plan to do.

Backup the whole WPMU install directory(or is wp-contents enough?)

Backup the database

Deactivate all BP related plugins in the plugins folder

Move out BP related plugins from the mu-plugins folder

Deactivate BP

Click the upgrade thingy for BP

Activate BP

Move/Activate the rest of the plugins

I’ll be doing this over the weekend. Hopefully all goes well as I am running it on a live site.

Thanks for your help guys.

Another newbie question..does deactivating plugins reset their settings? (I am guessing not)