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Being able to do a basic integrity check on a file before leaving it overnight to convert could save a lot of time. I recently discovered that ffmpeg could be used as a basic error check, and I was very surprised to find errors in many video files that were popular downloads of recent media.
What version of HandBrake are you currently running:
1.0.7
What operating system and version and you currently running (e.g. OSX 10.11, Windows 7, Ubuntu 14):
I doubt you'll find much developer interest in this, though I can't speak for everyone. I have a hard time imagining how this would integrate neatly with the typical HandBrake workflow, TBH.
I think your best bet is to use ffmpeg and then call HandBrakeCLI if you're satisfied that the input file is error-free.