"I am thinking I should leave the hives that are filling the upper deep alone as long as they have a empty super above their deep.
What will happen if they fill the upper deep then goldenrod blooms, will they go above the upper deep and store the golden rod in the empty super? I think golden rod is going to go crazy this year with all the rain we have had."
that's what i would do yankee, leave the upper deep alone with the empty super above. the bees will store the surplus in the empty. it might not get capped or fully capped, but you can use it to feed back to them if necessary.