The cooling fan on the extruder no longer turns on.

The thermistor is detecting the temperature.

I’ve tried swapping the left fan for the right fan.

I’ve tried replacing the fan

I’ve tried resetting the machine to factory settings.

How do I fix it?

Assuming the settings for it are correct in the EEPROM, it’s probably a broken wire or loose end-connection in the harness from the main-board to the extruder assembly. And if it’s not that, it’s probably the transistor on the main-board. Start by direct wiring a fan (or even a little light bulb or something) directly to the connector on the main-board. If it turns on, that narrows it to a bad wire or connection. You may even get lucky and find that the screw-terminal connector for it is just loose.

But, if the fan (or test light) won’t work there either, then it’s probably the transistor on the main-board that turns it on and maybe even a combination of transistor and wiring, as a short in the wiring could burn out the transistor. The transistor is fairly inexpensive and is available from places like DigiKey and Mouser, probably less than $1 (the shipping will cost considerably more than the part), but will require some rudimentary soldering skills to replace. Without the soldering skills to replace it, you’d have to resort to replacing the main-board or sending it to someone to repair it.

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