First, it sounds like you have some experience with brake systems, correct? If not, seek technical help. There are many shade-tree mechanics that have discovered their lack of knowledge leads to a bad situation.
You shouldn't have any worries about hurting the brake master cylinder as long as there is fluid in the cylinder's reservoir. Engine off or on makes no difference.
I do all my own work on my fleet but if a complete fluid change was desired, I'd take it to someone with the requisite equipment and skill to do the job. The size of a Class A brake system would definitely influence that choice.