Didn't quite understand your sequence of actions. Did you put washed kefir grains back into the separated whey/casein kefir or in the new milk?
Dpending on time kefir grains will eventually turn milk into whye and casein parts if you leave too long. Since grains are growing at a rate of 10% per 24h fermenting in milk it depends on amount of milk and grains when the separation will occur.
As far as rinsing itself I rinse grains just occasionaly when I notice protein deposits on grains acumulate.
So when you leave grains for too long and separation does occur you just rinse grains lightly and put in the next batch of milk or put in a small amount of milk and put away in the fridge. With separated kefir you can shake it tu put back in kefir consistency or you can drink (or discard) whey and make a very tasty cottage cheese from the "tofu" part of kefir- just put that "tofu" in a cheese bag, hang it, put a pot below so that remaining liquid could drip away. After a while you get superior taste cottage cheese and you can add your favorite add ons like fruits or anything you want.