There are two bullet connectors in the fan circuit that may not be fully connected causing the fan not to come on occasionally (short circuit). The fix is simple, the connectors are located in the rear of the quad near the relays under your seat. Underneath those three relays is a small plastic pouch. They are wrapped up so you will have to cut open the tape sheathing, push the connectors all the way together and then tape the sheathing back up.
Below is a copy of the factory Yamaha service bulletin.
Modded Raptor would like to thank BJH