Upon system restart, dconf editor doesn't save changes

Lock down specific settings

cited from GNOME Help/Sysadmin Guide/User Settings/Lock down specific settings

To lock down a dconf key, you will need to create a locks subdirectory in the keyfile directory. The files inside this directory contain a list of keys to lock. Just as with the keyfiles, you may add any number of files to this directory. Here is an example of what one might look like:

How to lock the default wallpaper

1. First, set a setting, such as a default background which will be used for this example.
2. Create a directory named /etc/dconf/db/local.d/locks.

3. Edit /etc/dconf/db/local.d/locks/00_default-wallpaper, listing one key per line:

   # prevent changes to the background
   /org/gnome/desktop/background/picture-uri
   /org/gnome/desktop/background/picture-options
   /org/gnome/desktop/background/primary-color
   /org/gnome/desktop/background/secondary-color
   

4. Update the system databases:

   # dconf update
   

As of dconf 0.7.4, lockdown is only supported on a per-key basis for performance reasons; you may not yet lock entire subpaths. There are plans to address this in future releases.

Your Solution

For adding to your new /etc/dconf/db/local.d/locks/00_default-touchpad file:

    # prevent changes to the touchpad
    /org/gnome/settings-daemon/peripherals/touchpad/natural-scroll

gnome dconf gsettings lockdown