CFR 1222 covering archival of Government communications was in effect from 2002, and State Department 12 FAM 541 to 12 FAM 545 covers sensitive but unclassified information (which includes things like meetings, schedules, promotions, personnel discussions) was in effect from 2005. She broke both of those, and they were in place for years before she was appointed SoS.
And if you had bothered to read these regulations you would see that she adhered to the letter of the law in both cases. An email was lawfully archived as long as she printed out the email or it was stored on a government server (any email she sent to government address would be stored on government servers, unless deleted by the recipient). The handling of senstive but unclassified information was in accordance with the law.