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In case, most of the stones have not been detected, it would mean that they have been eliminated.
Persistent pain in such individuals who have undergone lithotripsy and do not have any detectable stones, could be due to ureteral injury, associated scarring caused by movement of the fragmented renal stones.
You might continue to take the pain killers and antispasmodics prescribed by your doctor for the time being. With passage of time, complete healing may occur, and you will find relief from your symptoms.
In the mean time, continue proper dietary measures as well as increased fluid intake,so as to prevent further formation of stones.