One more question, you said "However, I want to be a 100% sure that in so doing I am not going to affect the main site of the sub-domain as,"
so are you moving wordpress from say example.com to blog.example.com ? And what do you mean by "not going to affect the main site"... because if your moving it, the main site won't exist. If your trying to clone one blog into another and have 2, then thats different. It's hard to tell exactly what you are trying to accomplish, I can read it more than one way.