It seems I am probably going to end up having to travel to get her treated.
I had a hope that someone would have had the same experience and it could be fixed by changing something simple like her diet...
Anyway, about her eyes. The vet did mention that she does have an incomplete iris. He also said he is not sure if that is normal for chinchillas (I don't know either). I have read though that it is normal for a dark beige chin to have dark red eyes.
Here's a pic:
The image is kind of dark, but her eyes are dark red with a light blue ring around her pupil. I guess the incomplete iris observation by the vet was in reference to her having a light blue iris and the rest of her eye not having pigment causing it to appear dark red.
The only test I had done on her was the stool sample test to see if she had parasites. The results were negative.
The vet recommended other tests, but I'd rather find a vet who has more experience work with her.