Last night, during imaging session I tested automatic meridian flip with EQMod driver. It went OK, except... just after the flip calibration data is reset and PHD2 starts recalibration before resuming guiding. Normally, I reuse calibration data between imaging sessions without any problem. It is also ok to use the same calibration data on both sides of pier.
So the question is - what's the point of removing calibration data and recalibrating after a flip? I don't think this action can be disabled by a user either.
BTW this behaviour might ruin guiding at all if your telescope is pointing near zenith... calibrating at high altitudes is far less effective and might result in guiding errors.