In looking into this a bit and thinking about it....
These files have binary zeroes in the riff header and data chunk. These files will not play in some media players and officially they contain errors because the data chunk counter does not match how many bytes are in the data chunk.
However, I agree that FLAC should be modified to detect and to handle this condition. Some of the better audio players like Winamp and Foobar2000 don't care about this and handle files like this without incident.
I doubt that Sound Devices will be processing files offline. It doesn't make sense to stop recording, recoup as much space as you can off of a media and then continue to record. It makes more sense to encode while recording. This is the main benefit of FLAC. That said, Sound Devices should not have the aforementioned file problem because they are not processing input files. They will have an encoder instance, and process files being provided from the converter.
That is not to say that there couldn't be problems due to power failure or whatever. I think that you should be able to decode through errors after the fact and get your data back. Yes, it's just one more thing that could go wrong, but users will have to weigh the benefits vs any additional problems it might possibly cause them.
I see it as a good move on their part.