If you are unable to perform a system update due to the Joy-Con controllers not being recognised, you can use the touch screen to connect to the internet and enter the required fields. If another Joy-Con works with the console, only the non-working controller will need to be repaired. While on the HOME Menu or on the Controllers menu, the Joy-Con controllers are not registered as being attached to the console.

Reset each Joy-Con by pressing the SYNC Button once. Then press any other button on the controller to power it on again.If your console is already up to date, be sure to restart it by holding down the POWER Button for at least three seconds, then selecting Power Options followed by Restart.

After attaching the Joy-Con controllers to the Nintendo Switch console, the console does not detect that they have been attached. If another Joy-Con is not recognised by the console, or if another Joy-Con is unavailable, the Nintendo Switch console and the problematic Joy-Con will need to be repaired. One controller or two, vertical or sideways, motion controls or buttons…Joy‑Con and Nintendo Switch™ give you total gameplay flexibility.If the Joy-Con is still not recognised by the console, try to detach and reattach it to the console a couple times. Detach the Joy-Con controllers from the console, and continue with the next steps by troubleshooting one controller at a time. If you can't remember the button mapping settings for your controller, you can set the console to sleep mode. Upon waking it, you’ll have the option to reset the button mapping.