The picture you added does help me better understand what you're asking. It looks like the branch in question is indeed part of the top graft, and not the rootstock. I believe there is a graft visible below it, but it's hard to tell for sure from here.
In this case it is just a question of standard pruning, and the information I posted above about doing so applies. There is a recently cut branch above this one at the top of the first picture which appears to have been done correctly, so copy that one if you want to cut this one off as well. Japanese maples don't like being pruned this way, but they tolerate it better the younger they are and the smaller the branch.
