There are several ways one could move the classified material, each almost too horrific to contemplate to anyone who has worked with sensitive materials. You need to understand that even discussing this gives professionals the shakes. There are a lot of serious things in the national defense world, but nothing is taken more seriously than classified material. People can and do go to jail for screwing up. Well, at least the little people do.
One way would be to download it to a portable medium, like a thumb drive. Leaving aside that you can’t bring a thumb drive anywhere near a SCIF, the USB ports on the computers are likely deactivated. You would need a technician to somehow work around that, which is in itself horrifying. The easier way would be to print the material out so you could take it somewhere else and either type or scan it into a new file on an unclassified system.
Of course, printing classified material and taking it out of the SCIF are themselves huge violations even before you get to not only reproducing it but introducing it to an unclassified system. So now the minion has contaminated the unclassified system, but there are still more steps to take and rules to break.
The minion could type text into the email, but that seems unlikely. More likely is that the minion opens the PDF of the classified document, which still retains all the classification markings. The minion then cuts and pastes some or all of the classified material, sans classification header, out of the PDF and into the body of an email, then sends it, unsecure, to Clinton’s unsecure server. This was an unsecure system where, it is important to note, she stored over a thousand documents containing classified material. And those are just the documents she didn’t delete.