Can you break-in two digital cables simultaneously using the same transport/DAC?Yes.
All that is required for normal current to flow through each cable is the presence of the termination resistor (or equivalent load impedance) in the corresponding input circuit of the DAC (75 ohms for S/PDIF, 110 ohms for AES/EBU). I can't envision a DAC design that would remove the termination from the unselected input, in part because the terminations and receiver circuits are separate and different for the two inputs. And as long as the termination is present, the transport would have no way of knowing which DAC input is selected (assuming the transport itself does not have a switch to select which of its outputs is used).
Disclaimer: This response does not imply an opinion as to whether or not the breakin process will accomplish anything.