I guess so, if you use a conversion tool that doesn't recognize the flags, and writes its own output, it can do that. There may be an option in those tools to force treating the input stream as using the full JPEG color range. In ffmpeg there's a -color_range option which should be:
0 == unspecified
1 == "MPEG" range
2 == "JPEG" range
Maybe it could be used to convert the videos to MPEG color range, so that other tools don't have a problem.