Isn't it possible that if you know roughly which parts of the registry you are going to be tweaking then you could use the registry library to extract the current settings and store them to a file.
Then you could make your changes knowing that you have a backup of the original settings. The only problem I can see that could arise is if you add new keys as this will change the array that B4PPC creates when getting the list of sub keys.
I haven't tried anything like this myself, it's just an idea.
Regards,
RandomCoder