If the problem occurs only while the fan is powered (not when it is spinning down), you could try setting Z probe type P9 in your M558 command, as if you were using a bltouch. That will cause the firmware to run deployprobe.g and retractprobe.g for each individual probe move. You could turn the fan off in deployprobe.g and on again in retractprobe.g. The Smart Effector only "hijacks the fan power" to power the illumination LEDs.

You may also find these wiki pages useful: https://duet3d.dozuki.com/Wiki/Connecting_a_Z_probe#Section_BLTouch https://duet3d.dozuki.com/Wiki/Test_and_calibrate_the_Z_probe https://duet3d.dozuki.com/Wiki/ConfiguringRepRapFirmwareCartesianPrinter#Section_Homing_Z_using_a_Z_probe

I tested it within several ways, which with bed compensation and it works great. Thank you to @dc42. You can mark it as solved.