Did anyone witness the removal of the broken hardware? The EMP would have destroyed the hardware (you know, where the actual electronic components are found), not simply glitch the software.
All of the hardware would have had to be replaced if EMPs actually do what they are purported to do.
Not necessarily. Lots of stuff will survive. In many cases just a power reset/reboot will revive a system. If there is real harm inflicted with enough power from the EMP, you may have fried components.