If it's not connected, it may not matter.But Dirac will try to correct that split and re-routed center channel, will it not?
Actually, what I do is to calibrate my system with a center channel but when I want to play the system without one*, I keep the same Dirac calibration/settings but:
1. Disconnect the center speaker/amp.
2. Before the Dirac VST in the signal, route/add the "Center" source to "Left" and "Right", both at -3dB.
*I will do this later this week so that my wife's Christmas tree can stand where the center speaker belongs. The speaker returns in early January.