I'm having a similar issue on my 2014 sportsman 400. I actually made a jumper wire to plug into the contact locations on the fan relay socket. Mine overheated this week, I pulled the relay and installed my jumper. The fan ran about 3 seconds and shut off. I then pulled the 20 amp fan circuit breaker out of the connectors and it was full of water. I'm not sure the water would be an issue but it seems my problem is the fan circuit breaker. It must be a little weak and when I ride the fan cycles on and off. I suspect that the thermal / auto reset breaker is opening prematurely. I ordered another breaker. I will waterproof it the best I can and see if the new breaker solves my problem.
I let my ride cool for about 10 minutes and drove it to my trailer. When I got it loaded and strapped down, I turned on the switch and the fan ran. This tells me the breaker had reset itself.