Hi Stone in kidney or stone fragments in kidney only very rarely causes pain. It will cause pain if it drops into the tube draining urine from kidney(called ureters). If CT scan is normal it it unlikely that there are any stones in the ureters without what is called hydronephrosis on CT scan. Some of the stones are very soft that they may be oulverised as powder by lithotripsy and all that the patient notices is cloudy urine. The flank pain could be due to bruising caused by the lithotripsy on the kidney and might take few weeks to resolve. Keep drinking adequate fluids and pain killers till then.