How to solve the problem of encoding with audio track 2 Handbrake CLI and Breakfast.app?

I think You should take a look at trac.handbrake.fr/wiki/CLIGuide#options, It has specifically audio options. I have tested this line, but a 2 should be sufficient for what you are asking. I must tell you the procedure. But If you some technical knowledge then only you will be able to understand it. It is as follows.

General Handbrake Options are-h, --help Print help -u, --update Check for updates and exit ### Destination Options are -o, output Optimize mp4 files for HTTP streaming -I, --ipod-atom Mark mp4 files so 5.5G iPods will accept them Set CPU count (default: autodetected) -Z. preset Use a built-in presetCapitalization matters, and if the preset name has spaces, surround it with double quotationstart-at Start encoding at a given frame, duration (in seconds), or pts (on a 90kHz clock) --stop-at Stop encoding at a given frame, duration (in seconds), or pts (on a 90. marks -z,Set output file name -f, --format Set output format (mp4/mkv, default: autodetected from file name) -m, -v, verbose Be verbose (optional argument: logging level) -C, Add chapter markers (mp4 and mkv output formats only) -4, large-file Use 64-bit mp4 files that can hold more than 4 GB. Note: Breaks iPod, PS3 compatibility. -O, optimize cpu Set input device -t, --title Select a title to encode (0 to scan all titles only, default: 1) --scan Scan selected title only. --main-feature Detect and select the main feature title. -c, --chapters Select chapters (e.g. "1-3" for chapters 1 to 3, or "3" for chapter 3 only, default: all chapters) --angle Select the DVD angle --previews <#:B> Select how many preview images are generated (max 30), and whether or not they're stored to disk (0 or 1). (default: 10:0) --start-at-preview <#> Start encoding at a given preview. kHz clock) preset-list See a list of available built-in presets no-dvdnav Do not use dvdnav for reading DVDs (experimental, enabled by default for testing) Source Options are -i, --input markers