Hi, Thanks for writing in. The stone while passing through the urinary tract might cause injury to the lining cells and this can result in pain and nausea persisting after the stone is removed. It can also be that some of the stones might have been too small on earlier scans and have increased in size during last two years. This can cause acute pain since the last two days. It is possible that the pains vary in intensity and severity depending on location and size. Drinking lots of water an fluids can flush tiny stones out of your system.