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Can I leave the built-in IR in my Smarther AC with Netatmo unconfigured in case I don't need it (example: installation with IR emitters where communication is via Zigbee)?

The built-in IR on the Smarther AC with Netatmo can be disabled or used in parallel with the IR transmitter to control an additional air conditioner. If you don't need it, you can simply skip its configuration during commissioning.