Nouns don't change gender. The definite article for feminine nouns happens to be the same as the definite article for plural nouns is all. It doesn't matter if the nouns themselves are masculine or feminine or neuter, all plurals take the definite article die.
So, die Augen means there are more than one neuter eyes. Not that eyes suddenly switch gender when there are more than one of them. (Not gonna think about asexual, self-replicating eyes, nope!)