MKV ToolNix will take MP4/M4V as an input. The output will be a MKV file.
That won’t be a problem for Plex. It will be a problem if you want to load the show into iTunes, which does not support MKV files…
Here’s two approaches to combine the files into one MP4/M4V file:
Approach #1: Use MKVToolNix & Subler
- Combine the files using MKVToolNix.
- Remux to a MP4/M4V using Subler.
Subler is Mac only. If you do not have access to a Mac, you can use ffmpeg to remux the file.
Approach #2: Re-rip, Combine, Transcode