Thanks for your query.Based on the facts that you have posted it appears that you have undergone surgery for kidney
stone. You have not mentioned about the nature of surgery whether it was a endoscopic surgery
like (PCNL OR URS) .
The pain that you are getting now is not related to previous surgery and can be due to recurrence of stone or due to spots in the kidney that you have mentioned in your query.
Please consult qualified Urologist
for clinical assessment and further treatment.