Part of the controversy is the concern that classified information may not have been stored securely, but another concern is that Clinton may have deleted email

Part of the controversy is the concern that classified information may not have been stored securely, but another concern is that Clinton may have deleted emails which legally must be preserved (the federal records act). Compare with the 2013 IRS controversy, which could not be properly investigated because Lois Lerner's hard drive had been erased.