MKV2M4V

you will need is just a professional MKV to FLAC converter named Avdshare Audio Converter.

MKV2M4V is a simple front-end to 'FFmpeg' and 'MP4Box'. It does a great job in coverting MKV video files to M4V video files. It is particularly quick for repackaging MKV files which already have tracks with the correct format for M4V. The conversion is quick, pass-through, with minimal CPU time. It has the advantage of being able to queue a large group of files and run the conversion all at one time. You thus don't have to babysit the computer for each file conversion. Just drag the whole group of files to the file-list pane. Set the parameters. Press Start and there you go. Come back when they are all done! Other converters force you to do one file at a time. Handbrake can queue jobs but it uses a lot of CPU power to do the conversion. When you don't need to convert the video, this takes a long long time to do. This is well worth $2.99. Heck, I spend four times for lunch each day. It could use more obvious interface buttons. For example "Enq", "Q" are very vague buttons.

Use Remux instead. It’s FREE and has many more capabilities than this. http://www.macupdate.com/app/mac/35968/remux

This is a terrific application if your goal is to go from x264/h264 MKV's to M4V files for your Apple products. MKV2M4V will pass through the video and either passthrough or re-encode the video as needed and as requested. I leave the setting for AppleTV which will convert a DTS to AC3, or if it is AC3 it will make sure it is at the right bitrate, and it also adds a second AAC stereo audio track, chapters are imported too. The Dev is adding more usability features, I'm so glad that I found MKV2M4V, no more encoding MKV's to M4V's, re-muxing is so much faster and better quality.

It’s simple, it’s cheap and it works straight away. You can complain about the price if you want to but I’m happy to pay $2 for the 100s of mkv movies I’ve got to be converted. Even if you had 10 movies, it’s surely worth that price.

There are at least 4 FREE apps which do the same thing (my favorite is remux). Though none of the free alternatives can convert FLAC streams in a movie file (at least not that I know of), I have NEVER, EVER seen a FLAC audio stream in a movie file (and I work with multiple formats from various sources every day). But, even if I were to find a FLAC stream in a movie file, there are several free tools that can be used to quickly and easily demux the stream (I like MKVTool), convert the audio independently to AC-3, AAC or whatever (my favorite is XLD), then remux it with the video stream into an MP4 file (I like Subler). Though some apps will only mux/remux to the .mp4 extension, if you simply must have the .m4v extension for iTunes compatibility (which, IMHO, is a horrific way to watch media, so I never use it), just change the .mp4 extension manually to .m4v (because the only difference between them is that Apple made the stupid decision years ago to force its native apps (like iTunes) use a proprietary extension.