"The work was partly funded by DARPA, with the hope of creating more advanced prosthetics for wounded war veterans."

Yeah, sure, that's what it's for, Mr. Sarin.

It seems possible that this magnetic affectation could be a cause of spontaneous damage the hard drive servo information.

This would cause one of the clicking-type malfunctions which you described, as that "clicking" you hear is the noise the head assembly makes when the drive is rapidly moving it back and forth across the platter attempting to get a fix.