I wouldn't even know how to begin answering that one, i have only ever tried to make a basic mission, i didn't even know you could merge
I would back up any file before you attempt that, so that it you do mess anything up you can easily replace the files you tinker with.
I know not great advice, but if someone has indeed done this before it would be reasonable to wait and hear from them before continuing with it.
Not to say don't try, just to be careful