Before you start, I'd recommend backing up your CFS3 directory just in case. So normally that would be "C:\Program Files\Microsoft Games\Combat Flight Simulator 3".
All you need to do is find it, right-click on it and select "copy", then right-click on the folder you want to back it up to and select "paste". That way, if it all goes horribly wrong, you don't have to mess around reinstalling the patches etc. to get back to where you were.
Every time I've got a good working setup, I back it up like this before adding any more new stuff. It takes quite a bit of space, so I've also been burning some setups to DVD. Also makes it much easier to synchronize everybody's setups for a LAN game.
When you install planes, the next time CFS3 starts up, it uses all the information about the planes you've installed to create a .bdp file for that plane, which it then uses to actually load the plane in future. It takes a while for it to do this, so it only does it once. This means that if you change a plane, it won't recreate the .bdp file unless you bring its attention to what needs doing by deleting the existing one.
The BDP nuker just deletes *all* BDP files from your CFS3 installation, so CFS3 will have to recreate them the next time it starts up. It will take a bit longer to start up that one time, but should get everything right.
Actually, I also run the BDP nuker before I do a backup, to save a bit of space.
Cheers,
Nick