The stages of chronic kidney disease (CKD) are based on two factors. First, is there evidence of kidney damage such as a missing kidney, abnormal findings in the urine, or abnormal radiology studies. If any of these are present for more than 3 months, it qualifies as CKD. Hence, with your missing kidney, you have CKD because of the reduction in overall kidney tissue and function. The second factor is an estimate of your kidney function based on a estimated glomerular filtration rate (eGFR). The eGFR is calculated based on a serum creatinine and other variables that are entered into an equation. You can review the equation at: https://www.kidney.org/professionals/KDOQI/gfr_calculator
Hence, your stage of CKD is then dependent on your eGFR and does not matter whether you have one or two kidneys. You can enter your data into the equation and determine what stage of CKD you have.