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Hi, Welcome to Just Answer. I'm Chris, a small animal Vet based in the UK. I am reviewing your question and will get back to you as soon as possible
Was the giardia proved to be resolved with a repeat faecal sample? Also how long has he been on the anallergenic diet?
We need to ideally treat until negative for giardia, if it is consistently positive this suggests reinfection either from other animals in the household, environmental contamination or the animals coat itself.
Giardia can damage the intestine lining and this can take a few months to full recover.
With regard to the anallergenic diet, if inflammatory bowel disease is suspected then we need to use the diet for 6-8 weeks as the sole diet (not other food at all) before the full benefits are seen.
Hmm, I would consider also getting a faecal microscopy performed to check that your cat is no longer shedding giardia.
I would also consider a blood test to check vitamin b12 as this may need to supplemented via injection
In my opinion she needs to be clear of giardia before the underlying extent of any GI disease can be evaluated.