Repacking Huffyuv/PCM AVI captures into MKV
 

I am currently capturing home VHS's using Huffyuv/PCM into an AVI container. Is there any downsides to remuxing these into an MKV file while maintaining the Huffyuv/PCM lossless compression? I am encoding a second copy in MKV/h.264/AC3 with chapter markers for distribution. My reasoning is, having the archive version in MKV would allow me to add chapter markers to the lossless versions. This would simplify automatically reencoding the complete collection if I choose to in the future. Thank you.

Not really outside of some applications not supporting mkv. I've used mkvs with ffv1 video + flac audio to squeeze down capture sizes a bit for archival. You can even use mkvs with avisynth provided you use ffmpegsource2("filename", atrack=-1) instead of avisource (though the ffmpegsource loader needs to index the file when loading the first time which can take a little while.) You do want to use codecs that ffmpeg support in the mkv files tho (huffyuv being one).

You can create the chapters file in MKVToolNix and save it as .xml. Then after re-encoding, re-multiplex the chapters file with the new video file. This keeps the original capture file untouched.