I figure this is not an unusual occurrance. I'm a bit surprised that Cosworth / GM don't have a simple tool to complete the write process for this exact scenario. Should be pretty easy for them to do, I'd think.
Turns out due to the way MP4 files are structured this is hard and it's not unique to the PDR MP4 files. Most of the tools ask you for another "valid" file to try to figure out what to add back to close it out and even then my luck has been slim getting the video back. Since I have no idea what's in the Marlin stream I'm hoping it's easier for Cosworth to provide a tool to extract it. I've known multiple people that have crashed with PDR running but not shut down the system gracefully. It would be great to be able to at least get at the data to help identify what happened.