As long as everything was drained and changed properly there shouldn't be a problem. Make sure to get it good and hot to burn off any moisture left over in the engine, and keep doing oil changes till the oil is not discolored.
Did you shut it down before it sucked in water? If not, should maybe do a compression test,.. if you did I don't foresee any problems.
Pull all the electrical plugs blow them out and apply dielectric grease to them.
I would look into snorkels if you are into that type of riding.
As long as you drained it and flushed out all of your oils, changed the plugs. Run it for a good easy trail ride and she'll be just fine.
The biggest thing to remember when sinking anything is to kill the engine, flush out all fluids again and again and again until you get all of the moisture out. Never swamp a unit and then let it sit before you drain/flush.......
Keep ridin that badboy, those Can Ams love a good soaking once and a while! Just make sure you got all the water out of the crank case and the top end of the motor, change the filter also. Check your rearends also for any water. My Outty has had a few swims and no problems as long as you do the maintaince. Heres some cheap advise, make sure you always take some extra oil on trips, makes the several oil changes cheaper. My gang likes to save 5000km oil from oilchanges for changing oil in drowned quads. I hope you don't say that you have no scratches on your quad next! lol