Not sure exactly about your local climate, but I am guessing the winters are very cold by my own local standards. This in itself is not a problem, more relevant is how long your winters are. Abbe Warre’s recommendation of over wintering on the two full boxes works fine in the relatively mild and slightly damp climate of Northern France and the UK. However, I have heard of 3 full boxes being the standard for some of the harsher states in the US. If I understand correctly, you have harvested the top box leaving the bees with two full and one empty box. If they are full of capped honey, there will be very little space for extra storage but yes, if you are not averse to feeding, it may just help to top up those two boxes. If that bottom box is completely empty and comb building has stopped that box should be removed for winter and replaced as soon as your spring arrives. They may well be fine through winter on those two full boxes but you need more local knowledge on that matter. As you have harvested that third full box which in hindsight may have been a little premature, I don’t see that you have an option. I hope this helps a little but more specific local advice will override anything I have said. Best wishes and good luck.