A lot of books tell you to switch out your combs every 3 to 5 years but I've heard old timers talk about combs they have been using for 10, even 20 years. It gets very, very dark and hard. The problem with older comb is the contaminates. If you have been treating for mites, SHB, etc. those chemicals can build up in the combs, not to mention pesticides & herbicides brought in with the pollen and nectar.
As to the empty bottom box, I find that is very common in my hives this time of year. I frequently reverse the boxes. And for my last inspection before I shut the girls down for the winter, I usually make sure all the brood frames are in the bottom box (sometimes I have to combine the brood out of the two boxes) and make sure there is plenty of honey in the top box as the girls will move up over winter.
Now you have the problem that you are using two different sizes of frames so you can't pull the honey frame with a bit of brood down into the bigger brood box. I use all mediums and no queen excluder so if I find brood up in a honey supper, I can move it down to a brood box, but usually I just let the brood hatch the girls will either back fill it with honey, which I try to leave them for winter.