Whenever the Krita snap is updated, Reproducible: Always
Damn, hit enter too early.
Don't know how to edit, but anyway. Whenever the snap is updated, Krita loads from a new ~/snap/something/.local/share/krita directory. It's not really user-friendly and quiet annoying to have to copy the old one to the new location. I don't know if Snap can be configured to share the configs between updates. But the way it is now, it's totally broken from a user perspective.
This is what Michael Hall told me: 29.09.2016-15:16 < mhall119> it should be using ~/snap/krita/<version>/ for saving user settings 29.09.2016-15:17 < mhall119> and those files will be copied over to the next version when you update So if that doesn't happen, it would be a bug in snap, not in Krita. There isn't much that we can do...