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tsMuxer and MKVToolNix not working with FLAC?

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Hi guys, help needed! So I wanted to make Blu-ray ISO from two mkv files. I tried tsMuxeR, naturally, but somehow what I got was a message "some tracks not recognized and was ignored" and a video without sound on the output. I tried  MKVToolNix in order to merge those two files in one and drop it onto tsMuxer again, trying to solve the problem, but the result was the same - no sound and an error message. The merged file was also kind of weird, as I tried to play it in VLC player, it stopped right at the spot where those two files were merged. ToolNix did show the audio was FLAC. So I take it neither tsMuxer nor MLVToolNix don't really work with FLAC correctly? Or what am I missing? I'm not too technically advanced, so I'd appreciate any input very much! 

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FLAC is not in the BD spec, so...

1) Extract the FLAC using MKVEXtractGUI2

2) Convert the FLAC to WAV/(L)PCM or DTS/AC3. Depending on the length of the files, it may be over the WAV 4GB limit. Reduce bitdepth/channels/don't use PCM/use a tool that ignores the header length.

3) Remux & author.

Issues===

Depending on if you want to join the mkvs, i'm not aware that tsmuxer can mke a BDMV from 2 mkvs unless they're joined. If you want to join them, make sure they're exactly the same codec & settings (and even then it may not work).

Joining 2 FLACs via mkv and then demuxing that will yield a broken file. convert to another codec 1st.

We assume your mkvs' H264 track conforms to BD profile & settings. If not, you need to convert that too.