Files Become 0KB on Seemingly Healthy Drive?

Hey guys, so I was re-encoding a bunch of files on my media hard drive just a few days ago via handbrake, I left for 2 days to meet someone in another part of the country, and when I returned an input file or two had went bad, and handbrake didn't even show them in the queue, where I am certain they were before. In their place a 0KB file was left. I've ran CHKDSK and there were absolutely no bad sectors, or any other notable errors. Smart data seems fine too. Any ideas?