Easily done in MP4Box or the yamb frontend, along with a bunch of other stuff.

+1 for YAMB
or DVBPortal MP4 multiplexer

Just wanted to acknowledge the helpful replies.

This question came about because I had to do a training tutorial for a software product at work; the intended location is YouTube.

I needed a screen capture tool and my gamer son turned me on to OBS for doing monitor capture:

Open Broadcaster Software

It's a pretty cool tool. The original thought was for me to walk through the training and record it, and then have someone with better pipes and stage presence redo the narration...thus the question.
But since OBS Multiplatform can capture to either .mp4, .mov, or .fls. I decided to record in .mov. I recorded several chunks and then used QT Pro to join them together. (Finally found a use for that $29 software!).
The weird thing about doing that, though, is that while the "merged" file plays fine in QT, WMP only sees one of the different clips' audio tracks; this is because QT Pro kind of stacks the audio tracks, instead of joining them end-to-end. So I had to use Vegas to render the audio as one file and then bring that in to QT Pro to replace the original segmented tracks.
I'm thinking out using OBS to record a video on how to do this, since it's a useful way to join .mov files without re-rendering and incurring quality loss.

So I did make a short tutorial to show you what I was talking about:

It can be done with Avidemux quite easily.

Quite a few 'muxer' utilities available..I usually use 'MeGUI' which allows you to replace an MP4 files audio w/o re-rendering the video. I typically use the (also free) Nero WAVE to MP4 (or .m4a) encoder prior to muxing the audio back in with 'MeGUI'

Thanks for making the tutorial. Levels are a little low but content is very informative. I've been using MSI Afterburner to screen capture because it was one of the few free screen captures that can capture at 60fps.

After watching some YouTube vids of OBS, I see that OBS can also capture at 60fps and seems to be much easier to setup than Afterburner screen capture which you almost need a PHD in engineering to get it to capture properly.. (;