Thanks everyone for replies!
I think I have found the problem.
The problem was that I did not use my Eneloops for a long time. I stopped actively shooting about two years ago. Though I have always kept my camera and flashes handy,
I was taking much less pictures then before, especially with the flash light. (I have moved to new place and had to spend my time on remodeling more than anything else)
Now, I have figured out how to do TEST mode on BC-700 and change current to 700. It did speed up the process a lot.
I have run TEST on all of my batteries and measured voltage right off the charger.
Some of them were 1.3xx, some 1.2xx and some 1.1xx
I ran those with lowest voltage through the TEST again and they are coming back to 1.2xx or 1.3xx
Then I measured voltage again after one day.
So far I have found two that has voltage gone from 1.2xx to 0.9xx within 24 hours. These ones I am running through REFRESH mode, but if I cannot revive them, I will just recycle them
Some of the batteries I using now do not hold as long as they used to, but at least I can use them for some short time. I think if I will recharge/discharge them more often - they might be back.
But if it is not, it is not a big deal.
Currently I have 2 flashes and 2 remotes that use 12 batteries a once. I have 24 batteries.
I will run for a week or so, but if I am not happy - I will just recycle half worst batteries and buy Amason Basic x12 - just to have my AAs in two different color for easier detection old/new batteries.
Thanks again, everyone. I could not resolve it without you.