Hey Stephen, it's Adam Steinmark from the Google+ community. My design is very similar in movement style to the BCN3D Sigma, I'd post a pic but the CAD is in a weird spot at the moment and it's not extremely clear. I looked at your posts on this forum and saw the following from the developer:
"The Duet can support multiple Z probes and let you switch between them, so although I am not aware of anyone having used an IDEX system with separate X axes and probes, it is possible in principle.
You could connect one Z probe to the E1 endstop connector (E0 is not free on an IDEX machine) and the other to the Z probe connector, and use probe types 5 and 6 in the M558 command to select which one. Or you could connect both to the Z probe connector and use an analog multiplexer IC to switch between their outputs, controlled by the MOD pin on the endstop connector, and use probe types 1 and 3 in the M558 command.
You would probe with one head/probe and save the height map for that. Then with the other. The G29 command on the Duet allows you to specify the name of the height map file, so you can use a different filename for each head. Then in the tool change macro files you would load the height map file for the head you are switching in.
Bear in mind that if you want to do ditto printing (print 2 copies of an object simultaneously), then you need to match the nozzle heights accurately.
Did this work for you?