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When an app is running, the 20706 will not respond to HCI commands on the UART. Any HCI commands sent to the controller will have to come from the embedded application.
In the audio.headset app, comment out the wiced_transport_init(&transport_cfg) in hci_control.c.
This will obviously disable the WICED transport and your application won't function as expected but you should be able to use MBT to send HCI commands.
I disabled the external serial flash (U2) with switches SW7 and found that MBT works.