Most of the examples I can think of are from older action canons and involve a Big Reveal with the damsel in distress whipping off her wig and turning out to be the male villain in disguise.

I just remembered there's a sort of averted version of this in The Silent Partner (1978), where the cis male villain crossdresses as part of the finale (we met him first in disguise) and the main character and the audience recognize him instantly.