Seeing as Lavabit handled encryption and decryption server side, the order could have required them to retain messages after decryption. Or, less insidiously, just required them to retain messages they received prior to encrypting them. In both cases, they wouldn't have forced Lavabit to put in a backdoor, just keep what they had already. (though if they only stored decrypted emails in memory, that distinction is small).

Remember, Lavabit voluntarily complied with other court orders, so they likely have the technical means to comply with what the feds want.