Of course, I ordered a new fan but it will take 2 weeks to get here. I cannot fix the old 4 pin PWM connector as it’s too small. Meanwhile, as I have the IO connector:
On the I/O extension, there is one PWM pin for usage: PWM14: PIN13 reference this: Edge2 PWM [Khadas Docs]
After that, its just making sure you get the appropriate timings for the PWM:
Nominal RPM is around 10600 RPM, so you would have an PWM period interval of 0.0028 Seconds or 2.88 Milliseconds and with 50% duty cycle mentioned by the datasheet of the fan.