Thank you for your detailed history, it certainly sounds like little Sarah has had her fair share of medical issues and I am sorry to hear that they are continuing to this date.
Sarah’s main problem currently seems to be contained to her urological system – bladder and kidneys with persistence of pyelonephritis and cystitis. Inflammation of the kidneys and bladder can potentially lead to an increase in WBC on urine cytology as you have found. The various antibiotics that Sarah has been on sound as though they have cleared any infection but until the inflammation is completely resolved she is at risk of redeveloping both stones and bacterial infections.
In cases like this, urine is often sent off for culture and sensitivity to ensure that there is no remaining infection or determine the best antibiotic to treat existing infection. Further investigation of Sarah’s kidney’s and bladder may involve endoscopic examination if necessary to give a better idea of what is happening within these structures. Lastly Veterinary small animal medicine specialists are highly trained clinicians and often best equipped to investigate challenging cases such as Sarah’s.