"I am thinking I should go ahead and take the mediums off, extract and put them back in my hives while we are having a flow?? "
you could do that vandy, if there is a flow on. also consider saving back a few in case of a dearth, cheaper than feeding sugar.
wm, if your bees are re-purposing the wax from the medium supers above, i would either remove it (they are either not ready for that space, or no flow on). are you feeding syrup?