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Question Are I/O channels 1/2 and 3/4 of the UnitY entirely disabled in extended mode

Answer
Yes and No. No - for the outputs: The slot output channels are the same in Extended Routing as normally.Whatever you have selected on the DIGITAL I/O page 3 will be sent directly to the optional UnitY outputs. (Except if one or both UnitY Engine outputs are routed to "Out5.6" and/or "Out7.8, if so the UnitY Engine output will be sent to the UnitY cards optional output (5.6 and/or 7.8) instead of the signal sent from the 02R). Yes - for the inputs. Neither the UnitY card nor the O2R can mix nor route the optional EXT INPUTS 1.2 and 3.4. These inputs are fed directly from the UnitY I/O-card to the slot connector on the O2R, and thus, they will appear on the wires for Mic1-4 (if in slot3 / Mic9-12 if in slot4). These wires ends in nowhere as you have selected "INT ANALOG" on the Input Signal Select page (DIGITAL I/O page 2).