Re: Brood in supers, now what?
EDIT - Started writing before the other answers appeared, apologies for covering some of the same ground.
Probably nothing wrong with the advice you got, but just there is not "one rule fits all" in beekeeping. Which is why people argue over things like queen excluders, they can be right, or wrong, depending.
Firstly, your honeycombs that now have brood in them, can be used for honey again. However they will be darkened by the brood cocoons, which can also leach into the honey and darken it, but still perfectly edible.
Management wise, if you put a box of drawn comb over a brood nest without an excluder, if the bees do not fill it with honey fast enough, the queen will move into it, queens always move as high as they can. So the natural order is honey top, brood immediately below the honey, then below that empty comb, and pollen.
If you continue to stack more boxes on top, the queen will continue moving upwards, unless the bees can fill them with honey faster. So this is dependant on the nectar flow in your area.
Your mentor presumably has local knowledge, and if he says the bees will get enough honey to force the queen back down into the lower supers, then presumable he is correct. However, if you don't want the queen going into the honey supers in the first place, use a queen excluder. I do, and have not noticed those who don't harvesting any more honey than me. Just, use wire excluders not plastic ones, the plastic ones are too restrictive.
44 years, been commercial, outfits up to 4000 hives, now 120 hives and 200 nucs as a hobby, selling bees. T (mostly).