If you run the engine without any shim on the valve, the keepers can come off the valve and the valve will fall into the cylinder.
Now, you say you removed "another .048 shim" - where are you getting these shims? The thinnest shim available from Polaris and KTM is 1.45 mm (0.05708661 inch) - the thinnest available on the after market is 1.20 mm (0.0472441).
Yes, when you can no longer set clearance because no thinner shim is available, you have to install new valves or get the valve seats repaired or both - always a good idea to do all 4 if one needs to be done. Curious, but it seems the RH intake valve always wears faster than the rest. Same can be said about Honda's, Kawasaki's and others.
Shop Owner and Mechanic with over 50 years experience