I’ve seen several different uses for Fan pins on this forum, and I’ve never read about using them being associated with disconnected communication. I have a couple of guesses about your problem.
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Guess #1: The disconnection is caused by electrical noise. If true, you might solve the problem by rerouting the cables, or by shielding the cables.
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Guess #2: You are somehow pulling significant current through the connection. The high current is pulling the power supply voltage down causing the SKR Pro to reboot. Are you pulling the current for the motor from the Fan pin? If so, an inductive load might pull high current on startup.