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A number of modern millimeter, sub-millimeter, and far-infrared detectors are read out using superconducting microwave (1-10GHz) resonators. The main detector technologies are Transition Edge Sensors, read out using Microwave SQUID Multiplexers ($μ$mux) and Microwave Kinetic Inductance Detectors. In these readout schemes, sky signal is encoded as resonance frequency changes. One way to interrogate these superconducting resonators is to calibrate the probe tone phase such that any sky signal induced frequency shifts from the resonators show up primarily as voltage changes in only one of the two quadratures of the interrogation tone. However, temperature variations in the operating environment produce phase drifts that degrade the phase calibration and can source low frequency noise in the final detector time ordered data if left to drift too far from optimal calibration. We present a method for active software monitoring of the time delay through the system which could be used to feedback on the resonator probe tone calibration angle or to apply an offline cleaning. We implement and demonstrate this monitoring method using the SLAC Microresonator RF Electronics on a 65 channel $μ$mux chip from NIST.