Do you have any pics? What is the humidity like in the aquarium? IF the humidity is fine, another possibility is that the damage was so severe it may take a little longer to outgrow it. If an animal is kept at excessively low humidity for a length of time this can occur and take a while to clear up. If its just low humidity, then all you need to do is increase it. I received a perfectly healthy snake (that had no history of ill care), that for reasons unknown to anyone, had dented eyecaps, it took about a year, but eventually they just disappeared. There was no explanation for that case.
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