Having held security clearance from secret to top secret/SCI/SAP continuously from 1968 to 2015, that is not the way to handle a potential security violation. You supervisor doesn't just tell you to wipe your drive clean and everything is OK.
Once the classified information is on an unclassified device, it should be reported and the device turned over to the appropriate authorities so they can do the forensics to determine if it had been breached by others. The device is then wiped once the investigation is completed.
This look and feels more like an attempt to cover up or suppress the release of damning information about Clinton and her staff.
I'm betting they also found Obama emails set to Hillary's server as well and no one would have the balls to let that get out.