all dry sump systems have a springloaded valve to prevent oil draining into the crankcase. The one in the Yamaha engine is contained the the right side cover and is a simple spring-loaded ball. The rubber seat is very cheap and easily replaced. Usually, it is the raised sealing lip that is damaged and not the ball seat at all. Either way, the oil can drain back to the crankcase over time. Unless there is a large puddle under the bike, assuming it to be your bike and there was oil in it last time it was used, the oil is of course in the crankcase. Where else could it be? If you can get it to start, just let is run at a quick idle for 5 minutes or so and check the level. No damage will be done.
If you don't know, drain the system entirely (as said above) and refill it as in an oilchange, pouring about 1/2ltr directly into the cylinderhead thru the back access cover for the intake valves. Put about 1 /2ltr into the oiltank and ride the bike sedately around to block for 10-15 minutes, then check the level in the tank.
If you do have a faulty checkvalve, replace it. You need the valve seat
93101-14092-00
and a gasket for the side cover if you were not careful removing the cover. You can just as well put the cover on with a silicon gasket maker without a real gasket. I only do it this way.
http://65.213.72.112/tds5/docs/5926-EN.PDFIn a pinch, you can supplant the damaged raised lip with the silicon.