The fuse (that you are describing) is the only fuse in the entire system. It's purpose is to remove the battery from the rest of the harness (except the high current lug of the starter solenoid) in case of a short. When the fuse blows (if the engine is running at the time) and if the short is intermittent enough, the engine will continue to run using the charge circuit as it's power supply instead of the battery.
SO if when the fuse blows the engine stops. the short is still there and you may be able to find it more easily. IF the engine continues to run, and you just can't start the bike again later (the battery has been disconnected from all the electronics except for the starter solenoid), then the short is intermittent and it's going to be harder to find.
I seriously doubt it's the solenoid (starter relay), but if he's sending you a free one, at least that will eliminate the solenoid as the issue.
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'04 Suzuki LTZ400
'16 RZR XP4 1000 Turbo