Your system information
Steam client version (build number or date): Aug 19 2022, 01:534:24
Distribution (e.g. Ubuntu): Debian
Opted into Steam client beta?: Yes
Have you checked for system updates?: Yes
I'm having many of these same issues. I managed to be able to delete the controller config using comment 5 on this thread
https://steamcommunity.com/discussions/forum/1/1621726179577658947/
however that doesn't seem to solve the problem that the controllers refuse to combine even when the option is checked

Ah, thank you. I just deleted the following lines in Steam/config/config.vfd while steam was closed:
050000007e050000072000000xxxxxxx,dev:xb1:Joy-Con (R),platform:Linux,a:b0,b:b1,y:b3,x:b2,start:b9,guide:b12,leftstick:b11,leftx:h0.8,lefty:h0.1,lefttrigger:b4,righttrigger:b5,
050000007e050000062000000xxxxxxx,dev:gen:misdetected joycon,platform:Linux,a:b16,b:b15,y:b17,x:b14,start:b9,guide:b4,leftstick:b12,leftshoulder:b6,rightshoulder:b8,leftx:a1,lefty:a0,
And started it again, that seems to work.
Replying to https://github.com/ValveSoftware/steam-for-linux/issues/8726#issuecomment-1221109072
Your system information
Steam client version (build number or date): Aug 26 2022, at 21:00:42
Distribution (e.g. Ubuntu): Pop!_Os 22.04
Opted into Steam client beta?: Yes
Have you checked for system updates?: Yes
I have the exact same problem, I was able to connect my joy-cons to Steam, but they won't combine even after deleting configs, unpair them, rebooting the computer and steam multiple times.
Your system information
Please describe your issue in as much detail as possible:
Impossible to undo the config, so I'm stuck with a non-fully-working configurationProbably the main issue, but there is a workaround