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Please help.. Slow recovery after chronic coccidosis?

My holland lop aged 4 years was diagnose with coccidosis. The treatment lasted for 5 months inwhich we are struggling to clear the infection with the meds. The exotic vet suspected that the reason she keep getting pain from gi stasis was due to the infection that was not cleared yet. So last month we adjust her dose of metronidazole and another anticoccidal drug. She receive metronidazole for the whole 4 weeks which was longer duration than it was suppose to be given. And finally, the vet say that theres no more infection in her poop and say to do supportive treatment with cisapride, meloxicam and probiotics.

However she keep getting these flare up of pain (gi stasis) after. Its been around three weeks after stopping the anticoccidal. I’m so confused right now to the cause of it. I manage to wean her off pain and cisapride but she keep getting these episodes where one day she looked in pain (looked zoned out but her amount of poop is normal and she is still eating timothy grass still) and after giving her meloxicam for one day she was absolutely normal the next day and for the next 7 days. So its like I needed to give her meloxicam once every week due to these flare up. The last four days she was fine without the medication but today she sit and looked zoned out which looked like shes in pain with her eye squinting and the cycle goes like this….

The question is.. is it normal to have these flare up of pain after coccidosis treatment?? Is it her intestine trying to adjust??? Its been 3 weeks already and I’m really panicking to whether she got reinfected or not or the infection was not cleared properly but last 3 week and last week the stool was cleared , no coccidosis was found.

More information is shes on only timothy hay diet right now. She have sensitive stomach that cannot handle pellet well so we strictly give only timothy hay. Her amount of poop was always normal since the treatment. However, during the process of weaning somedays she still have one or two double poops per day, and sometimes few small poop, and soft poop (not cecotrope) otherwise the rest is all normal.

I am out of idea , it beens so long for the treatment and I’m panicking why she isn’t normal yet :( Blood test was done a while and everything came back normal, dental check was also done and doesnt seem to have problem relating to the flare up pain.
 
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