Had the messages been contained on a secure server, subsequent classification could occur while the entire cache of message was still contained. Residing on a hard drive makes the that a bit difficult.
Classifying something retroactively seems a bit odd though. If they were on her personal server, not the "official" one, then the messages were already "out in the wild" with no chain of custody. Then again, a previously non-classified message could have been printed and distributed to someone who wouldn't meet the current qualifications for access, so the horse could be well out of the barn already.