Did they do the x-ray then? Was there a test done that showed there were stones? How can they say they were there, but couldn't be identified.
When I took Sigmund in the vet they told me that sones can be different sizes and all through out the urinary track, even crystaline. Maybe it's the crystals that can't be identified on an x-ray, but they have some way to test for something the system creates becasue they are present. Just guessing; I'm not a vet. I wish I could help you more. Our vet also said that a lot of alfalfa in the diet could cause problems.
Unfortunately for Sigmund his stone was too big. We tried surgery and had it removed, but he passed away the next day. He was 4 years old. Maybe the ones your boy has will pass through the system without problems. Did they give him any pain meds? I don't think they just go away on their own.
I hope he'll be ok.