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Yes, she could. The fact that you are no longer in the service isn't legally relevant. What matters is what your rank was and her rank was at the time of conception, because that acts as the nearly fool proof evidence of the relationship.
This works the same with any criminal offense. We look at the situation at the time it occurred and subsequent facts, while sometimes relevant, don't entirely change the determination.
She could technically be punished under the UCMJ.