Today I updated my game and for some reason all the bonus cases were locked and all of my progress (regarding bonus games) was lost when I unlocked them again. Has anyone else had this problem?

Yeap, the current download seems botched - it states version as "Update 4" but contains basically the original game without bonus content (it's 30Mb smaller than "Update 3" that I had downloaded on August 14).

I have raised the issue with GOG Support yesterday, no reply from them as for now.