What a turnaround, Oguz. Losing both colonies and then filling both hives again from swarms, one of them moving in on its own, plus honey at the end of the season. Congratulations, that update made my day.
Alessandro mentioned varroa as the most likely cause last winter, so I'm curious: are you doing any mite counts this autumn, even if you don't plan to treat? A sugar roll doesn't hurt the bees, and it would at least tell you what each colony is carrying into winter.
Full disclosure, I'm asking partly because I'm building a small beekeeping app called Smokebook. You log an inspection with a few taps, it turns a sugar roll or sticky-board count into a mite load and compares it with the guide value for that month, and each hive keeps its own curve through the year. Whether you treat stays entirely up to you. Most apps assume you treat, so I'd really value feedback from someone keeping bees the natural way, and honestly I'm not sure yet how well it fits a Layens hive. If you or anyone here would like to try it, send me a purple moosage and I'll email you a free code.