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I have two videos, one without audio (the second). Trying to merge them gives this error:

mkvmerge concat1.webm +concat2.webm -o output.webm
mkvmerge v5.8.0 ('No Sleep / Pillow') built on Oct 19 2012 13:07:37
Automatically enabling WebM compliance mode due to output file name extension.
'concat1.webm': Using the demultiplexer for the format 'Matroska'.
concat2.webm': Using the demultiplexer for the format 'Matroska'.
'concat1.webm' track 0: Using the output module for the format 'VP8'.
concat2.webm' track 0: Using the output module for the format 'VP8'.
concat2.webm' track 1: Using the output module for the format 'Vorbis'.
No append mapping was given for the file no. 1 (concat2.webm'). A default mapping of 1:0:0:0,1:1:0:1 will be used instead. Please keep that in mind if mkvmerge aborts with an error message regarding invalid '--append-to' options.
Error: The file no. 0 ('concat1.webm') does not contain a track with the ID 1, or that track is not to be copied. Therefore no track can be appended to it. The argument for '--append-to' was invalid.

Is there a way to instruct mkvmerge to simply extend the first audio track?

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AFAIK you cannot do this with mkvmerge alone. When I had this problem, I used ffmpeg to add a silent audio (with matching sample rate, number of channels and bits per sample). The following example adds silent mono audio with 48 kHz sample rate to a video without recompression.

ffmpeg -i in.mkv -f lavfi -i "aevalsrc=0::s=48000" -shortest -c:v copy out.mkv

See also:

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