I get the same running rdr2 through steam OS and whenever i wake up from sleep and toggle my bluetooth, the game no longer recognises the controller.
Steam Deck
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See my edit. It's a bug in Proton 10. Don't use Experimental or Hotfix at the moment.
i noticed this happening too with ffvii rebirth. turned out to be an issue with proton, because the issue disappeared after i switched to the latest proton-GE (9.2X or something around that number)
Yes, that was it! It's a bug in Proton 10.
There's apparently an issue where this is happening in some games running through proton 10 (or proton experimental because that uses proton 10). Recent steamOS updates apparently helped fix it for people, but that probably hasn't helped you since you're not on SteamOS.
I would recommending forcing your steam play to use proton9 or lower until it's fixed.
That sounds like it may very well be the issue. I think I'm running Proton Hotfix at the moment.
I wish there was a way to see what Valve did to fix a problem with SteamOS. I'm also interested in their solution for low memory slowdowns.
I run it on SteamOS, bought via steam. No problem on my side so far.
I also run stuff via steamos so I cannot tell much from your setup. However, maybe there is a trick that could potentially work. On the steamos, when you are on to desktopz it is possible to switch between desktop mode and gamepad mode controllers (not sure on exact naming here). You can do this by pressing for a second or two the upper right button from the front (I believe the legend is 3 stripes or similar). On the steamos it changes modes and can help you unblock controls on weird situations.
Maybe this can help?
It helped when I ran a pirated copy through Heroic. I have since bought the game and use Steam Input, so I only get the controls recommended by Steam.
I will try replicating the desktop setup. Maybe switching out of the game and back helps.