I poked around a bit more, and found this in the Handbrake Documentation:
“They are the exact same file, the only difference is the extension. MP4 vs M4V.
For MP4 files, HandBrake will automatically use the extension M4V when you pass-through audio (AC3), use SRT subtitles or have chapter markers enabled.
You can simply change the file extension between .mp4 and .m4v as the file is exactly the same. There are no differences in the content or container itself.
You can disable the option to automatically set this in !HandBrakes preferences.”
Hope that helps,