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Illness/Sickness: Gills shrunk, possible eye damage(?)

I think this is a fair assumption. The previous replies suggesting that opaque lenses are associated with morphing in axolotls were misconstrued.

All I said was axotlotls don't typically have webbed feet
 
It is important to remember that many symptoms can be caused by a number of possibilities and so it is not always the best to rush into conclusions. Symptoms such as cloudy eyes and loss of gill filaments are more likely to do with water quality or husbandry than morphing.

Anyway, I think we can put that discussion to rest and move on and help the OP out. Below is a link on cycling you may find helpful

Caudata Culture Articles - Cycling

Do you have tests for ammonia and nitrite?
 
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