I’m hoping someone can help me. I’m a second year beekeeper and my first year’s goal was basically just keep them alive. Well, some February 2017 not only were they alive, the boxes were full of nectar! I did start a new package and split off my original hive. I also re-queened my original hive in May. They took to the new queen famously and I still had plenty of frames filled with honey. My honey super was completely full of honey, so I wasn’t feeding my hive. This hive seemed to be doing really well. Come July I did an inspection and noticed that the honey super was still full, there was plenty of brood and pollen in the bottom brood box, so I added a new brood box a queen excluder and left the honey super. I went away on vacation and did another inspection at the end of the month. The queen was still doing well, there was still honey in the super, but no comb was drawn on the frames in the new brood box. I went on another vacation and just checked my hive Aug. 13, still no comb drawn out, still plenty of brood, I saw my queen but there was absolutely no honey or nectar in my hive! I’m concerned because autumn is just around the corner and I’m afraid there will not be enough honey to get them through a New England winter. I really thought I would get to harvest this year so I’m really surprised. Does anyone have any idea???
Sounds like a swarm left… 
Other than that, have you done mite counts? Any photos?
I thought of the swarm, but this was after I already split off the hive and the queen is still there…I actually found her this time 
I thought of the mite count, I’m getting plenty of brood on the bottom box and I did do a mite count and do need to treat…but what about the honey? I think that’s odd…there is absolutely no honey left in my boxes and I had a whole honey super full! Can a high mite count affect the honey disappearing?
Honey disappearing is a swarm, absconding or robbing. This time of year is high risk for robbing, low risk for swarming and some risk for absconding, depending on what your bees are unhappy about. I had a hive abscond last year at the end of September, due to Argentine ants. I don’t think they are a worry for you, but the principles hold true. 
Robbed? You can get silent robbing with no fatalities. I’ve seen it a few times
Or perhaps a dearth has begun and the stores have been greedily consumed?
2 of my hives have done this in the last month. We have had a very wet July. Has rained almost every day. Queens still there but no honey. I started feeding sugar water with Honey B Health added and they have started filling back up and capping off. The queens have started laying again. I removed the upper honey box until they refill the bottom super. This same thing has happened to several other local bee keepers this year.
That sounds like what’s been going on here too and I ended up doing exactly what you said. I fed them and took off the honey super. When I checked the hive again a week later, the comb was being drawn out and it looked like they were producing honey again. Do you think that they just ate the honey because it was too rainy to forage?
Survival mode by eating their honey storage was the consensus of several ‘Old Timer’ bee keepers I know. Luckily we checked hives when we did. I learned an important lesson of watching them closely during the July, August flow when we normally think of there being an abundance of pollen and nectar.
I am constantly learning something new
And learning what weather conditions cause a dearth of nectar.
It’s usually rain here 
But a drought causes the same problem.
Good that you found them in time
How does one know if there is a nectar dearth in general, besides watching bee actions.
How long does a nectar dearth typically last or is it the end of nectar until the next spring?
Should I be removing my flow hive super (no honey is being stored in it after being on for the first time for a month.) and feeding my bees more sugar water now to help them build up honey for the fall \ winter? (In Missouri).
If you are member of a local bee club, you can ask the locals. In much of the US, the main nectar flow is over by early to mid-July. Some areas have a second flow in Fall, depending on what trees and shrubs are in your region, but it is minor for most people.
If you have a hive scale, you can see the hive weight starting to drop, like this chart of my Arnia monitor:
Otherwise, if you keep detailed inspection records, you will see the frames gradually emptying over time. If there is no nectar flow at all, a deep frame of capped honey will last an average hive about a week to 10 days, depending on how active they are. If they are still foraging, they use more. If they are clustered for winter, they use less.
Yes, and yes, if they don’t already have adequate stores. They will need 40 to 80lb of honey to get through the winter without feeding.
Thanks
My hive is 2 boxes deep and the flow hive is the third box. I inspected all boards last week (8 in 1 box and 9 in the other). I saw 4 boards appeared to be primarily honey with some honey on the tops of some of the others. I’d think that is not near 40-80lbs of honey though.
They appear to still be foraging. They are constantly flying in and out like crazy most days. I see some bees coming in with pollen on their hind legs but not the majority of them. I cannot tell if \when bees are carrying nectar.
How exactly do I go about getting the bees off the flow hive box \ boards to take it in for storage until next year?
While they are not storing anything in it, there are many bees all over them all the time. Do I just take the box off and set it aside the hive and expect them to all fly out and back to the main hive?
The arnia scale looks really interesting but it is too costly for me right now considering I just invested in the Flow Hive this year too. I’m just a private 1 hive owner with no expectation of making money off this. I just want to help grow nees and maybe get some honey for myself next year.
If it is truly empty, then yes, you can take it off the hive, set it on end a few feet from the hive, and most bees will leave it by the end of the day. Don’t do this if there is any unripe honey in it though, or it may provoke a robbing frenzy. In that case, I would use a bee escape board or a fume board to drive the bees down.