Have to see it live to be sure, but it sounds like potentially you're getting an update while the machine is running, and you haven't rebooted to load the new GPU module.
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Had that problem recently, apparently the (nvidia) gpu driver version of the system and the one within the flatpak need to be exactly the same. Ran a flatpak update and it worked again.
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I dont know, maybe its some kind of mandela effect i got, because i do need to update flatpak after system update. Maybe i just didnt update flatpak and didnt noticed everything not working until hours later, because lightweight apps didnt run as slow or had graphics bugs.
That's the main reason I created desktop launchers that use Nvidia together with the program no matter if it's needed or not, maybe you should try it
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