I'm sorry for both you and Mika. It's so difficult not knowing and thinking the worst... I tend to do that too much as well
Nookie is going through something similar as well. About 6 weeks ago he started showing the signs of a bladder infection, so he was put on a 10 day course of Clavamox. A few days after it was done, the symptoms came back, so he was put on Amoxiclav for 21 days. Last Saturday, he started with the usual urination urgency/frequency that he gets with an infection, and he was still on the antibiotic (the last dose was Monday morning). He does a lot of whining/pacing and is very unsettled when he has an infection (he has always been prone to them). So we took him back to Dr. Marsden on Tuesday. He had only been off the antibiotic for a little over 24 hours, so I was thinking a Urinalysis was probably a waste of time and money, and it may have been, at least in part, as they did not see any signs of infection. What they did see, however, were several Struvite crystals.
We are quite familiar with bladder stones as Thorin had them as well. He never showed any signs of anything being wrong at all, until I saw him pee blood
I think I mentioned this before, but his stones were calcium oxylate. The only way to get rid of them was surgery. He had one lodged in his urethra. The blood was caused from that and also the stones in his bladder. They were pretty jagged and had cut up the inside of his bladder pretty bad.
If your vet hasn't done an xray yet, that's the very first thing I would ask him to do. Thorin had a few "pee tests" that didn't have any crystals, so just because your vet isn't seeing them in the urine doesn't mean they aren't there. They will cause the inflammation, bleeding and can also cause secondary infection, but not always. Nookies recent (and seemingly difficult to get rid of) bladder infection is probably caused by the struvite crystals. Dr. Marsden did suspect cystitis as well and put him on a Chinese herbal supplement for the swelling/discomfort and it did help.
Nookie has also had the sterile sample taken quite awhile back. He's a HUGE wimp (seriously... BIG baby lol. Screams like he's being killed if he stubs his foot while playing), but he seemed to handle it very well
Good luck!!