Was pre-riding some of Saturday's ride of the 2 Day Algonquin Trail Ride and hit a submerged rock in a muddy puddle and tipped over. Unfortunately the bike went over on the airbox intake side and I was not able to get to the kill switch before the bike stalled. Pushed the bike out of the water and removed the air filter. We gently kicked the bike over manually to make sure it was not hydrallically locked and it seemed OK. Tried the starter but it wouldn't make it past top dead center. Filter was wet so we pulled the tank, pulled the plug and tripped the bike over. Some water came out the spark plug hole. Since I have a Resluse I used the electric start to pump the rest of the water out. We then poured a little gas down the spark plug hole and started re-assembly. After a few tries we got the bike running with the kickstarter. Rung out the filter and reinstalled. We finished off the pre-ride (about 40km) and I then washed the bike, replaced the air filter and cleaned out the airbox as best I could. On Sunday I pre-rode the main Sunday loop but the bike did not sound exactly right when I started but I could not determine what was exactly wrong. Finished the ride with no problems with the bike though it did not sound normal and loaded up for home. At the first opportunity I dropped the oil with was grey and then I notice the collasped oil filter. Not good. With a new filter and new oil I fired the bike up and almost immediately heard the knock from the bottom end on idle. It seemed OK with some revs but as soon as it returned to idle the knock was quite noticable. I am in the process of removing the motor and will report back when I know more but I am not holding out hope for a cheap fix.