Additional info:
I was able to recover upgraded armor by restarting the game and loading game saved before today. So lost progress of ~40 minutes. A bit better than loosing all the resources, but it already happened twice so it looks like this is a recurring issue.

I purchased Ultimate edition with free Berserker pack (bonus content - settlement, longship, armor). I've played 34h so far using full Berserker set and already twice I had situation when I open the game and Eivor is wearing only underwear and I get message that I unlocked bonus content. I have to apply manually all the armor, runes and everything I was using.

I've already upgraded all of these armor parts with ores and leather (4 levels each) and when they are unlocked again, they are not upgraded - I lost ALL THE RESOURCES which I invested in upgrading these part (around 700 each).

This is ridiculous.