They never had the plaintext of the messages in the first place, so they don't need to delete them. That's what end-to-end encrypted means.
In the former case, Facebook can decrypt the messages at will, and the e2ee only protects against hackers, not Facebook itself, nor against law enforcement, since if Facebook has the decryption key they can be legally compelled to hand it over (and probably would voluntarily, going by their history).