On Pixel 6a with the latest version of GrapheneOS installed, this is what I do and this problem occurs:

  1. Create a second user profile
  2. In that user profile, location is disabled and I add PIN.
  3. I use it to browse things like Gmail, Instagram, etc. (with Proton VPN installed).
  4. After I am done, I switch back to my main profile by clicking on the user icon in notification panel.
  5. After going back to main profile, I delete second user profile.
  6. I turn off Multiple Users.
  7. Reboot phone.

Upon rebooting, the quick settings get reset to default, all my customizations have disappeared.