Question

How can I encode and concatenate multiple videos using HandBrake / HandBrakeCLI??

In HandBrakeCLI when I run:
HandBrakeCLI -i file1.MPG -i file2.MPG -o out.m4v -O -e x264 -r 23.976 –pfr

the output only contains the second file!

Answer 1

You cannot concatenate 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 details.

Once the videos are concatenated, you can encode them however you like.