The reason the government compartmentalizes information like this is that from looking at the data one can determine the source. That makes her email server an extremely grave vulnerability the entire time it was running.
If you stand back and look at the whole picture....it’s mostly about the dozen-odd people around her. Remember Syd? He was supposed to be hired and given a clearance within the State Department, but the White House said no on Syd. I’m guessing others that she also wanted to hire....were denied. So when her team sent her the ‘big’ emails with classified...Syd was within the Foundation team and likely getting the same email and could respond to help Hillary understand what was going on.
This wasn’t so much about Hillary being stupid (she is), but the whole team created this server idea to provide info to the non-cleared members of the foundation helping her future strategy. I think when people start understanding this...it’s just Hillary who is in trouble....there’s probably a dozen characters who looking at a court appearance.