Whenever the system is rebooted the gnome settings are applied notification shows up and resets most of my changes

so after installing garuda linux I went through the setup , installed updates upgraded it to the ultimate edition installed the missing firmware for linux-zen and after that I rebooted the system and all the ui customizations I had done were gone

Check to make sure you are not accidentally logging into the Guest Account

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I have removed the guest account

Are you on a laptop? I have managed to remove the default customizations on default garuda while messing with gpu drivers. Perhaps you need to get the prime render offload compatibility package for linux zen.

Search for GNOME 40 in forum.

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