Unfortunately the PNL may not have gotten all the stones. And stones can "hide" on xrays and other tests. CT is best test but these are expensive and have alot of radiation compared to standard xray.
I am a recurring stone producer and have not had a "clear" kidney for 14 years. They have never completely gotten all stones out. I had the PNL once- and never will ever again. I've had multiple lithotripsy and also had ureterscopy. Had good results with ureterscopy. They did this when I was suppose to have litho but when they did the prelim xray, they found the stones were stuck along the stent they had put in. Eventhough I had called 2 weeks before and asked if the stones could pull the stent out they said no. There were 6 pieces in ureter between kidny & bladder.
Hopefully they will test the stones they removed to see what they are made of to determine if change of diet will help. There is also a thyroid disorder that can cause stones so ask your urologist to test for this.
Mine is a genetic predisposition as it runs in fathers side of family. I have changed my diet and restricted many things. Plus am on medication to try and prevent more from forming.
Best think for kidney stones is drinking lots of water. I heard real lemondade is suppose to help but no proof.