Additional observations:
1. Custom shortcuts are preserved.
2. Seems that settings are stored in ~/.config/dconf/user and it's content is changed when I change shortcut preferences. This file stays the same until I login again.
As an attempt for workaround I changed permissions of ~/.config/dconf/user to read-only and after login this file is overwritten anyway.
Additional observations: dconf/user and it's content is changed when I change shortcut preferences. This file stays the same until I login again.
1. Custom shortcuts are preserved.
2. Seems that settings are stored in ~/.config/
As an attempt for workaround I changed permissions of ~/.config/ dconf/user to read-only and after login this file is overwritten anyway.