Here's a chronology of NARA rules on keeping emails from personal accounts.
Prior to 2009, using non agency email systems was not addressed.
In 2009, NARA ruled that it did not outlaw personal email accounts. This was the first year Clinton was sec. of state. NARA specified that federal (not personal) emails sent on a non agency system " must be preserved in the appropriate agency recordkeeping system."
In August 2013 -- after Clinton left State -- tNARA issued a bulletin that personal email can only be used in "emergency situations," and when used, the emails "are captured and managed in accordance with agency record-keeping practices." and "Late last year -- long after Clinton left the State Department -- President Barack Obama signed an update to the Federal Records Law to prohibit the use of private email accounts by government officials unless they copy or forward any such emails into their government account within 20 days."
Read more about it here http://www.cnn.com/2015/03/04/politics/hillary-clinton-emails/index.html