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Thank you for your question. My name is***** I have been a small animal veterinarian for 13 years.
Have they found blood in the urine when they take the urine directly from the bladder with a needle (cystocentesis)? If the blood is only there when she urinates and not present in the urine in the bladder then it may be coming from the vaginal tissue. Vaginal problems would be exceedingly rare in a spayed dog, but if they have not found anything with all the tests they have done, the next step would be to use an endoscope to evaluate the vaginal vault. They could have polyps or they could have some conformational change that is causing urine to pool in the vaginal vault and cause irritation. They could also just have irritation there for no detectable reason.
That being said, they have done an extensive workup and ruled out all the serious problems so it may be worth trying some benign neglect (meaning you don't worry because it seems like nothing serious is wrong, but you monitor it, if it is getting worse then you looks again). Procedure like the endoscopy I'm talking about have some risks... you have to sedate them so risk of the sedation and some risk of vaginal trauma for the scoping.
Another thing that you can do is try some probiotics. We have found that dogs that are prone to vaginal irritation often have imbalances in the vaginal flora so feeding the 'good' bacterial in probiotics can help right that. I like Fortiflora, but any probiotic could work.
I hope that helps, but if you have additional questions please ask. If not, please rate my answer.