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Honestly, without knowing what it did, I would just do a factory reset reimage (Thanks PopinFRESH). Maybe what it did was harmless, or maybe it was a terrible exploit that gave your Steam Deck e-cancer. You can't really know for sure, so one way to be certain.
I'd personally do a re-image rather than a factory reset. If whatever it was had root privileges and was making changes to GRUB it would not be unheard of that if it contained malicious code that it would persist after a factory reset. Without knowing what the code specifically did there is no way to know if there is anything malicious or not. You can't really postfacto determine what occurred via logs, etc. as it was given root level access so it could do whatever and remove whatever was done from any logs.
A factory reset doesn't wipe the OS, it wipes the user account and resets specific settings. A re-image will completely wipe the system including the bootloader (GRUB).
This is the same reason, as an example, for linux servers that have been root compromised the only real solution is to backup the data and do a clean install of the operating system after nuking the existing filesystems. Otherwise you have no idea what backdoor(s) have been left in the compromised system.
I found some more info here.
https://lwn.net/Articles/705877/
If thats the case and you've already done the factory reset, just re-do the same steps and select to re-image instead as you're already at relatively the same point but without wiping the OS filesystems. It doesn't take too much longer to redo it as a re-image; and its not something I'd chance my Steam library on; especially with 600+ games like yours.
Here is the Steam Deck Recovery Instructions for creating the USB flash drive (UFD) and booting from it to perform the re-image. If you use cloud saves for any game you'd be playing on Steam Deck then you'll be no worse off and it'll automatically re-sync your saves once you re-install any games after re-imaging.
If you decide to re-image it and need any help beyond that support doc feel free to ask and I'd be happy to help.