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So did Creality screw up and reverse where the part fan and electronics fan plug in on the Ender3? Stock has the electronic fan in the FAN0 slot and part cooling in FAN1. If I set fan speed to 0 it would shut off the electronics fan. I simply switched the plugs and now I can turn off my part fan when needed. How the heck did they miss that?
I do not know how engineers can make such mistakes.
Though something similar happened when I purchased my 3D Printer, where the exturder stepper motor was running backwards.
Rewiring the Stepper motor cable fixed the problem, Have upgraded Marlin firmware from 1.1.0 - 2.0.3 and have deturmined the wiring is correct.
the 2 fans are reversed when switching from the stock board to SKR board. I'm guessing that's where your issue came up. It's unfortunate they advertise as a direct drop in replacement, but don't document that one difference.
as far as stepper going backwards...yes, swapping the wires will correct it, but if you're updating the firmware anyway, it can also be changed in Marlin.