When i connect my official joy-con and Pro controller wirelessly, they always disconnect when I open minecraft bedrock on Nintendo switch. I have tested my controllers on other games and they work perfectly but not on minecraft. Because the wireless controllers disconnect, I have to use handheld mode. The wireless controllers disconnect when they're in handheld or tabletop mode but it works when it is connected to the TV.
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Thank you for your report!
We're already tracking this issue at MCPE-54533, so I will resolve and link this ticket as a duplicate.
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Can confirm, controller does not work when on table top or handheld mode, works when using the dock.