Chronic Kidney Disease (CKD) with Simple Renal Cysts: The presence of atrophic kidneys and multiple simple renal cysts, as indicated by the ultrasound findings, suggests a chronic process affecting the kidneys. Simple renal cysts are common in the aging population and can be associated with CKD. The lack of hydronephrosis or stones reduces the likelihood of obstructive causes, and the negative UA makes infection less likely.

Nephrolithiasis with Small or Radiolucent Stones: Although the ultrasound did not show visible stones, small stones or those that are radiolucent (e.g., uric acid stones) might not be detected. The patient's symptoms of unrelieved abdominal and flank pain could be consistent with a small stone causing intermittent obstruction.
Pyelonephritis or Interstitial Nephritis: Despite the negative UA, it's possible for urinary tract infections or interstitial nephritis to present with minimal or no bacteriuria, especially in the early stages or in patients with certain types of infections (e.g., tuberculosis).
Renal Infarction: This could present with acute flank pain and might not always show up on a standard ultrasound. However, the chronic nature of the patient's symptoms and the absence of suggestive findings (e.g., elevated lactate dehydrogenase) make this less likely.

Renal Cell Carcinoma: Although the cysts described are likely simple, any renal mass has the potential to be malignant. The presence of atrophic kidneys and multiple cysts increases the complexity of the diagnosis, and any solid components or irregularities in the cysts would necessitate further investigation.
Polycystic Kidney Disease (PKD): While the ultrasound findings could suggest PKD, especially with multiple cysts, the absence of family history and the size of the cysts might make this less likely. However, PKD can present later in life, and the diagnosis should be considered, especially if there are other systemic manifestations.
Aortic Aneurysm or Dissection: Abdominal and flank pain can be symptoms of an aortic aneurysm or dissection, which would be a medical emergency. The absence of specific findings on the renal ultrasound does not rule out this diagnosis, as it primarily affects the aorta.

Tuberous Sclerosis Complex (TSC): This genetic disorder can cause renal cysts and angiomyolipomas, which might present with similar symptoms. However, TSC typically has other systemic manifestations and is less common.
Von Hippel-Lindau Disease: Another genetic disorder that can cause cysts and tumors in the kidneys, among other organs. It's rare and usually has a family history and other associated findings.
Medullary Cystic Disease: A rare inherited disorder characterized by cysts at the corticomedullary junction, leading to chronic kidney disease. It's less likely given the description of the cysts but could be considered in the differential diagnosis of hereditary kidney diseases.