That's because she made sure they were removed, disproving her claim to the FBI that she was ignorant of what the markings meant.
(See here for Hillary's bald-faced lying to a US Navy veteran at last night's Commander in Chief forum.)
When Jake Sullivan complained in 2011 that he couldn't send something to Hillary because of a classified material header, she told him to remove it and send it non-secure, as recounted by HotAir already in early January here, where the email is reproduced. It took her all of four minutes to commit a crime.
Why are we still rehashing this? Hillary should be under indictment, not running for office.
In a thread from June 2011, Hillary exchanges e-mails with Jake Sullivan, then her deputy chief of staff and now her campaign foreign-policy adviser, in which she impatiently waits for a set of talking points. When Sullivan tells her that the source is having trouble with the secure fax, Hillary then orders Sullivan to have the data stripped of its markings and sent through a non-secure channel. ... “If they can’t, turn into nonpaper w no identifying heading and send nonsecure.” That’s an order to violate the laws handling classified material. There is no other way to read that demand. Regardless of whether or not Sullivan complied, this demolishes Hillary’s claim to be ignorant of marking issues, as well as strongly suggests that the other thousand-plus instances where this did occur likely came under her direction.