Good to hear.
This vet sounds very on top of it. When there are recurrent UTI issues or one that won't go away, it is important to culture and culture again..and again...and again
until you know it is gone.
Infection going to the kidney - very possible. A lot of times pyelonephritis dogs act sick. Doesn't mean it's not possible though. She is young. It would make sense since the UTI was mismanaged by the previous vet.
U/A and culture should come up bacteria free if taken cysto. Any remaining from an infection means there is still an infection that needs to be treated. Good thing this was caught now because kidney infections can be so serious.