Mosfet usually fail always on (or catastrophically to the point where there is nothing left of the part)

So if the fan works on the always on output but not on Fan0 before and after the replacement its not untinkable the fault is elsewhere, unfortunately the next part in the chain is the main processor (FAN0 goes straight to pin 90 on the ATSAM4S8C)

To further diagnose verify the part has connectivity from the Gate to R42, from the Drain to Fan0- on the header and from Source to ground. Then (with power on) check if you have a gate signal on either side of R42 with respect to ground when the fan is turned on.

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I have a electronic shop nearby, they have lots of stuff, i will look tomorrow

I would be interested to find out what component needs swapped out. I have some experience soldering, but not sure if it's worth attempting to fix without knowing more first.

Like I said I was able to get everything working on Fan2 so not a huge concern for me currently.

@Voxles
the duet switches on the negative. the positive gets the voltage directly from vin.

Solution!, I had checked literally everything and replaced everything, turns out it was the wire, I set my multimeter to continuity mode and found that there was an internal break in my + wire connecting to the fan, looked intact and was the only other part I hadn't replaced, now that thats gone and a new wire is in place I am up and running with it, so it seems anyway!

Thanks for the support guys!

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.

I presume you have connected the input of your integrator to the FAN- pin of the FAN0 connector. Did you also connect a pullup resistor between FAN- and +5V?