Ok folks. You have all been so helpful but here is what happened now…
This amazing, thriving hive went down to just a few thousand bees. Over the last couple days I saw ZERO activity
So i cracked the hive open today… horror and dismay is what followed. They are all dead. I am not sure how it happened, but they are literally all just dead. Take a look. Any ideas how i can figure out what i did wrong?
Hi Chris
I’m not sure, but it looks like your queen in the second photo (dead on the top of the frame) however, if it is the queen, she only died recently. Perhaps the numbers got so low they couldn’t keep warm enough?
Dang, i didn’t even notice that. I was pretty sad over it all. It did get cold here over the last 2 weeks. I guess that is very possible. UGH how horrible
Hi Chris,
So sorry for your loss. The most common reason for colony demise in late fall or early winter is varroa. As @Dan2 says, if the the numbers dropped rapidly, the survivors can then not keep warm enough to survive. However, it would be most likely that varroa killed your hive by dropping the bee population too low for survival. There is a very good article about it here:
https://beeinformed.org/2016/03/08/why-did-my-honey-bees-die/
Did you do mite counts? Did you treat? If so, what did you use, and when did you do it (what month)?
Edit - I just checked your old posts. You treated with Apivar, no mite counts, and the treatment was late in the season. I still think that the treatment was probably too late to save them - it would have helped more in August. I count after treating too - mites often come back in large numbers in Fall if the bees have been out robbing other hives which are collapsing from Varroa. I have recently had to retreat my bees, even though I treated them fully in August. 
As usual thank you @Dawn_SD. I already got the mite kits for next year and will try again in spring. At least the new hive will start with TONS of honey. Both supers are heavy with honey. Maybe i can do better next year.
Should I clean out all the dead bees and just leave the hive for next year or is there anything I should do for the winter now?
I shake out what I can but don’t go ocd over it. The bees will clean that out much faster and better than we can.
Thank you sir! I will do this later on or tomorrow and leave a fresh hive for next year.
Don’t forget to protect the hive from pests but leave a little ventilation if possible.
I have a entrance reducer on the front already.
I agree with @Anon on shaking out dead bees (and brushing the bottom board clean), but I would say that your entrance reducer may not be quite enough once the hive is fully dead. Depending on design, it may not keep rodents out, and they love to build in unprotected hives. Also, if there is honey in there, wax moths, robbers and possibly SHB may take the supplies before your new colony can enjoy it. I have some good robbing/migration screens which can be used to close the hive completely, but allow air flow:
http://www.brushymountainbeefarm.com/8-Frame-Moving-and-Robing-Screen
Failing that, I would close the entrance with #8 hardware cloth (or smaller mesh) or even staple insect screen over it.
http://www.brushymountainbeefarm.com/8-Mesh-Hardware-Cloth-1-Linear-Ft
You have a good attitude, and your experience will pay off next year. 
Thank you again @Dawn_SD. Good idea on the mesh wire to close off the entrance. I will get some of that and fix the hive up and get it full winter ready. last thing we need is rodents in there.
Thanks!
Yes looks like PMS
There are one or two brood cells with cappings torn open. Have a look inside one of those to see if the bee inside has deformed wings.
There are spots of varroa poo at the tops of some of the cells
You have to monitor for mites regularly
UGH. I thought the treatment would kill them off, but instead i did it too late and killed the bees and left the mites… dang
Onward and upward. Keep going for next season.
Very important to make sure your winter bees aren’t compromised
But it sounds like you have learned from it, and that will make you a much better beekeeper for next year. Don’t give up. Beekeeping isn’t that hard, but it isn’t easy either. That is partly what makes it so fascinating. 
Thank you. I am not giving up. Just a little disheartened. but it will be better next year.
Also don’t get too upset about it-it’s very sad when bees die, but when you think about it millions and millions of bees die every day, and millions more are born and it’s been going on for 65 million years like that.
Every time I go into my yard now I see the odd bee scrambling around on the ground getting attacked by ants - fighting to the bitter end. I try to save them but most times nothing can be done it’s just cruel nature.
Jack, the sad part is losing the colony. Bee mortality is a fact of life, losing a colony IS sad. The good news is: it can be replaced next season.
