Notes

Some notes: INPUT.mkv is the original videofile, INPUT.dts is the original but external audiofile, OUTPUT.ogg is the converted output from INPUT.dts.

If I make a short fragment using the original INPUT.mkv and INPUT.dts and with a ｢-c copy｣ or ｢-c:v copy｣ parameter, then it either has an audio desync problem, or a mute portion of audio at the beginning of the file. With reencoding, the fragment seems to be building fine, but the goal is to make a lossless copy (without re-encoding).

If I use OUTPUT.ogg, no matter what I do the file will have desync problems.

ffmpeg -i test001Vs.mkv -i 001_testFrag002.ogg test114.mkv
	test114 (desync, merging short files, ccopy).mkv
ffmpeg -ss 01:06:26.739 -i "INPUT.mkv" -t 0:00:25.942 -ss 01:06:26.739 -i "OUTPUT.ogg" -t 0:00:25.942 -map 0:0 -map 1:0 -c copy test115.mkv
	test115 (synced, but no sound in front, c_copy)
ffmpeg -ss 01:06:26.739 -i "INPUT.mkv" -t 0:00:25.942 -ss 01:06:26.739 -i "OUTPUT.ogg" -t 0:00:25.942 -map 0:0 -map 1:0 test116.mkv
ffmpeg -ss 01:06:26.739 -i "INPUT.mkv" -t 0:00:25.942 -ss 01:06:26.739 -i "OUTPUT.ogg" -t 0:00:25.942 -map 0:0 -map 1:0 -c:v copy test116.mkv
	test116 (sound is ok, but video is not lossless)
ffmpeg -ss 01:06:26.739 -i "INPUT.mkv" -t 0:00:25.942 -ss 01:06:26.739 -i "OUTPUT.ogg" -t 0:00:25.942 -map 0:0 -map 1:0 -c:v copy test117.mkv
ffmpeg -ss 01:06:26.739 -i "INPUT.mkv" -t 0:00:25.942 -ss 01:06:26.739 -i "OUTPUT.ogg" -t 0:00:25.942 -map 0:0 -map 1:0 -vcodec copy test117.mkv
		test117 (synced, but no sound in front, vc_copy)