Looks like it happened when I used SettingsDeleteScenes.cs plugin to delete some obsolete scenes. It adds buttons to delete scene or package when you press small gear icon in the scene browser.
I had maybe less then half amount of old backups, and there is a trim option for SSD in windows, so there is no chance to recover the files.
Hopefully I'm using small amount of scenes, and mostly just change appearance presets which are placed in different location then scenes.
now I'm making backup of addonPackages, Saves\scene and \Custom\Atom\Person\Appearance\
Lessons learned
I had maybe less then half amount of old backups, and there is a trim option for SSD in windows, so there is no chance to recover the files.
Hopefully I'm using small amount of scenes, and mostly just change appearance presets which are placed in different location then scenes.
now I'm making backup of addonPackages, Saves\scene and \Custom\Atom\Person\Appearance\
Lessons learned