the problem is a simple one. The ECU (computer) is reading your engine temp and expecting to manage the fan to deal with it. The fan has a tach wire that reads out the RPM of the fan. The ECU depends on that tach reading in order to tell if and how fast the fan is turning. When it doesn't get that signal because the fan has been hacked to run manually, it gets no feedback from the fan's tach wire. To the ECU the fan is pooched (shorted out or open circuit) - hence the P0480 code.
There are 2 ways you can cure that:
1. by reconnecting the fan's tach line to the ECU and leaving the power manual. I can't tell you which wire is that one.
2. By reverting the manual hack and rewiring back to the original ECU-controlled fan circuit.
In either case you will need the shop manual for that Can Am to see where that wiring is and where it needs to go.
Good luck..