The scion needs to have sap flowing through the understock, because it is not fused initially enough to pull sap from the tree on it's own. So if you graft a shoot to a branch, you must keep green out at the end of the branch, or above the scion if grafting to a trunk to keep sap flowing past the scion. Once the scion takes, the branch or trunk can be shortened.
Note, grafts don't fuse immediately, some may take 3 years before it is safe to remove growth past the scion. Some fuse quick and one year is enough, takes experience and observation to know. It is safe to give more time, no need to rush removal of the understock's growth past the scion.