We moved into an apartment with a roofdeck in Chicago (near the lake, so zone 5b?) last summer and I was determined to grow fruit trees. I planted (in 2 ft. resin pots): Brigitta/Patriot/Bluecrop blueberries; Caville Blanc d'Hiver Apple on M26; Spartan Apple on (I think) M26; Morello and Montmorency cherries on Gisela; Scarlet Sentinel Columnar apple; Golden Sentinel Columnar. Perhaps some of your are laughing already--I know it was ambitious.
The trees started their life on a large, partially-shaded balcony until we moved to the roofdeck in August. The cherries were nothing but problematic: mildew (I think) and mites all summer. The other trees had similar, but less severe problems. The blueberries did the best. I decided to wait to see how/if everything survived the winter before deciding to get rid of anything.
Winter comes and goes. I figure out I should try a dormant sulphur/lime spray to combat fungus, so I do in January or February. I prune a few branches in March and to my delight and surprise I see everything inside is green. The cherry trees start to bud out tremendously. Everything looks on track. Then we have a snowstorm in April, followed shortly by about a week of very wet weather. I notice my cherry buds have turned crunchy. A little research reveals most of the twigs on my blueberry bushes have twig blight. As of today, the columnar apples look dead with no buds. The 1/2 of the Montmorency that did leaf out now has wilted, diseased-looking leaves. I still have hope for the Spartan (leafed out somewhat), Caville Blanc d'Hiver (no leaves, but does not look diseased), and the Patriot blueberry, which has several twigs of healthy-looking green leaves even after I pruned out the blight.
Thank you for your patience if you are still with me. My questions for this audience are:
1. Why do you think I had such extreme fungus problems? My varieties? The weather sequence? My inherent conditions? Pot conditions that could be improved?
2. How can I tell if the columnars, Caville, and blueberries are dead or whether they will eventually leaf out?
3. What should I be trying to grow instead of what I have tried already?
Wow... I've only guesses, and you've such a wide variety of fruiting plants and trees I don't know that any one thing would apply. Plus - I'm not very good with diseases ... after a quarter century of doing this (at the same location) - if anything needed a lot of spay care - it's gone!
I wonder if that shade gave you an initial fungus problem? I'm not sure what kind of humidity you have over there?
There's the bark-scrape test; starting near the dead ends, scrape away (not whittle) the bark down to the wood. If you hit vivid green, there’s still some life; if the green is mixed with brown, it's likely in the process of dying. Since everything's in pots, there's no hurry (I suppose) to 'replace' them. If I have a dead tree this time of year I insist on replacing it ASAP so as not to lose any growing time. You could squeeze in another pot, or not.
I have an overall guess, and it's a real problem when growing in pots: death by freezing. Most of us don't consider freezing weather will penetrate from all 'sides' of a pot, whereas if they're in the ground it only freezes from the top down... Here in zone 6 I'll "plant" my potted plants in winter by grouping them together and piling plenty of soil over & around them for insulation. Some I've actually planted the pot in the ground! Your losses seem too drastic for any one malady, other than possibly frozen roots..? I know you get a lot colder than we do!
...But maybe these ailments fit a profile familiar to someone else... if so, speak up! …This was simply my first thought 
If my guess of “death by freezing†is correct, just like my discarded pile of yearly pruned 'water sprouts' - if you scrape their bark it remains green for months after removal, even after the hardest of freezes. I suspect the living cells in the top part of the trees / plants stay 'viable' after their roots are severely frost damaged. But with no supply of nutrients from the the roots they will eventually die, or starve to death.
Though speculation... it's unlikely any other single 'agent' could have caused such consistent and permanent damage to your wide variety of plants 
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