On Linux, a native build will not recognize wired controllers if plugged in during the program's run. 4 situations have been tested, and none of them work:
- If any wired joystick disconnects and you reconnect it.
- If all wired joysticks disconnect and you reconnect them.
- If you start the Linux build, then connect any wired controller.
- If you connect additional wired controllers during the Linux game's run.
The best workaround is to be sure all the wired controllers you want to connect are connected before you start the Linux game, and make sure none of them disconnect.
This problem does not exist for wireless controllers. That assumes that wireless controllers disconnect by means of having the battery removed. That does not assume that the wireless receiver was unplugged. If that's the problem, you will experience the same issues as for wired controllers.