You cannot combine videos using HandBrakeCLI.
You can concatenate videos simply if they are in MPG-1
Using FFMPEG you can do
ffmpeg -i input1.avi -same_quant intermediate1.mpg
ffmpeg -i input2.avi -same_quant intermediate2.mpg
cat intermediate1.mpg intermediate2.mpg > intermediate_all.mpg
See the FFmpeg FAQ for more details .
Once the videos are concatenated, you can encode them as you like.
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