The only idea I have is from a one time experience with a UTI that was extremely stubborn to get rid of. I'm not even sure this will help at all as Peanut is already on Baytril.
Tinkerbelle had one and yes there was blood eventually. I took her in and they prescribed clavamox. Things went fine she finished the meds and then went for the retest and all clear. Then about a week later it came back with a vengeance and she was taken back, she was vomitting now, slowly dehydrating and lethargic, it was really quick. They kept her did all sorts of tests, xrays, you name it. They were baffled. This was my very first experience with a UTI ever.
They switched her to Baytril shots, once a day for a week because of the nausea she seemed to be having from oral meds. She actually had another shot so nothing would upset her tummy.
They decided that either the Clavamox was not effective with her UTI or that she was sensitive to it in a bad way.
I noticed an improvement within 48 hrs. with the blood and straining.
She recovered quickly and fully after that. I just wonder if it's the same with them as human's, sometimes one medication will work for one person and not another. I'm wondering if a different antibiotic would work.
I'd run that one by the vet.
I hope they get to the bottom of this really quickly, it's heartbreaking to watch them suffer like that and not know what to do.
Get well soon Peanut!