Currently unplayable on controller on Linux for me. I can't perform ANY other action while walking with the analog stick: using the instead dpad it functions as a workaround. However, when holding the right trigger on my controller, no other inputs are registered either, causing me not to be able to perform actions I was supposed to be able to do. And remapping the controls does not work either. Figuring out the last part, made me realize why I was stuck for hours, not being able to progress.

This is a problem entirely isolated to Silksong, no other game I ever played on this system has this issue. Launching the game through Steam and enabling Steam Input doesn't help either.

This is with an Xbox One controller. With an 8BitDo U2C, the game keeps ignoring the release event of buttons, causing all kinds of issues, and with an off-brand Switch controller, I have the same issues as with the Xbox One controller, just with the face buttons inverted. To top it off, rebinding the controller buttons either doesn't do anything, or crashes the game.

This is on the following system:
Operating System: Nobara Linux 42
KDE Plasma Version: 6.4.4
KDE Frameworks Version: 6.17.0
Qt Version: 6.9.1
Kernel Version: 6.16.4-201.nobara.fc42.x86_64 (64-bit)
Graphics Platform: Wayland
Processors: 16 × AMD Ryzen 7 5800X 8-Core Processor
Memory: 32 GiB of RAM (31,3 GiB usable)
Graphics Processor: AMD Radeon RX 7800 XT

Edit:
Turns out changing NativeInput doesn't affect the issues ...
For some reasons, starting inputplumber via systemctl, trying to start the game via OpenGamePadUI (which fails) and then stopping inputplumber, unplugging the controller, plugging it back in again and then starting the game appears to fix the issues until the next system restart. I do not know enough about inputplumber to explain why or how. So I didn't try to see if the "fix" survived through restarts.

Original message:
I managed to fix the ignored inputs on Xbox controllers as follows:

Open `$HOME/.config/unity3d/Team Cherry/Hollow Knight Silksong/AppConfig.ini`.
Change `NativeInput=1` to `NativeInput=0`.
Save the File.
Restart the game.

The off-brand Switch controller also is fixed by disabling native input.
This also fixes the issues with remapping of controller buttons in the game.

The issues with the 8BitDo U2C persist even after this change though.

This fixed it for my GameSir controller probably.

The description is that no simultaneous analog and digital input works. You can either use analog + triggers or button clicks. You can jump but to use joystick to move you have to let go of jump and vice versa.

EDIT: Nevermind it was just a coincidence. It sometimes work with input normally and sometimes not. This setting didn't fix it.

Using xpadneo solved these issues for me.

FWIW the original Hollow Knight's Linux release has had serious gamepad input issues from the beginning that were never fixed, and have now transferred over to Silksong. I wouldn't expect them to be addressed. Ended up Protonning the Windows release.

Edit: lmao now I'm having an issue where whenever I heal the controls die for 5+ seconds and I haven't changed anything since a few days ago when it was working fine (via Proton). Outstanding.

Turning off NativeInput is not enough, you also need to export SDL_GAMECONTROLLERCONFIG of your controller