I am happy to say that Houdini is almost recovered, he has no bald spots, he's quills are still a little bit sparce.
Shortly after I posted here, he's skin got better and he was no longer flaky, also he stopped losing quills. About two months after that, he got he's first new quill, I was so happy to see it. After that new quills started to come in slowly, 2-4 new ones each day. Two weeks ago all of a sudden, I saw hundreds of new quills coming in, now they are all full grown quills. Now he gets a fiew new ones every day, and I am sure that soon my hedgey will have all his quills back.
Turns out, that he did have nutrient deficency, and not mites. I did not ask for Revolution, since he got better after I posted, but if he had gotten worse, I would have asked my vet for Revolution. I did change he's bedding to fleece liner, he likes it and it is more convenient for me too (less cleaning and it does not get stuck in he's quills). I still give him Sunshine Factor, but I am not sure, how long I should continue it, I think I will give it to him untill he's quills are all back, and then ask my vet, what to do next.
Although it is winter and the air is dry (due to electric heater), he's skin is really good, not flakey at all, so I think all the flakeyness he has ever had, was not due to dry air, but the nutrient deficiency.
To all of you out there, having similar problems (and you are sure, that it is not a skin disease or mites), just be patient, because recovery can take a really long time. For my hedgehog, it was nearly a year. I do regret that I did not give him Sunshine Factor right away, when he's skin was just really flakey. Next time I won't make that mistake again. Hope you will learn from my mistakes