Minecraft does not respect the Nintendo Switch controller order.
If you start Minecraft while using joycons and decide to swap controllers, you will lose control entirely in-game unless you use the original controller that you booted up the game with.
Very easy to reproduce:
Start Minecraft while using joycons.
Connect another controller - in this example I'm using the pro controller.
Change grip order and set new controller (pro controller) as player 1.
A work around is removing the joycons from the console unit (turning them off entirely).. this should not be required tho.
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Cleaning up old tickets: This ticket had been set to 'Awaiting Response', but has not received a response from the reporter (~3 months+) so is being closed as Incomplete. If you feel this is still a valid issue then please comment, or create a new ticket following the Issue Guidelines which includes steps to reproduce the problem.
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Is this still an issue in the latest version?