Pull out what is left of the CAT and install a "D" plate. You can get a chip to fool the sensor. Look for the parts here (scroll down and look for CAT sensor chip and D plate):
YAMAHA GP1200R
Instructions for the install are here (pretty easy):
http://www.rivaracing.com/instructions/ry1819.pdf
You have to put in the plate to provide some restriction in the exhaust system. The engine will not run correctly without either the CAT or D plate.
Yamaha sold the ski to overseas customers with the "D" plate rather than the CAT, so it is perfectly safe, and may even run a little better.