Hi.
I just recorded a .mkv video with OBS Studio 25.0.8 (64-bit). After recording, I used the remux feature to get a .mp4 file. Because of my settings, I have the .mkv file have my mic audio, while the .mp4 file has the desktop audio. I confirmed this by playing them seperately.
However, when I put them both in Shotcut 20.06.28 (64-bit), both files play the mic audio.
Why do they do this? Is there a way to fix this? Is this an OBS or Shotcut-related problem?
Welcome here. We look forward to helping you. 
The .mkv file has two audio tracks?
Can you give data on the two video files where the audio tracks appear?
Any additional data would be helpful, for example a screenshot of the project.
In OBS, I set my recording file to .mkv, then set audio track 1 to my microphone. Track 2 was given to the desktop audio.
After recording, I remuxed the .mkv file, which only recorded audio track 1, into a .mp4 file, which only recorded audio track 2.
When I put them both in Shotcut, both the .mkv and the .mp4 played audio track 1.
Yes, I see that in the project, the two videos have the same audio wave.
Are you familiar with Shotcut?
If you place it over the track of each video you can get the properties of each clip. There is an icon on the top toolbar to get that information. 
Now I can’t access my copy of Shotcut to guide you.
It’s late here and I’m going to bed. 
Tomorrow I will continue with your incidence if it has not been solved by a colleague.
Shotcut only loads one audio track per video track.
Click on the clip, then Properties, click on the Audio tab.
2 Easy solutions.
Load the same clip in another video track (Above V1) select the different audio track, and hide the video with the eyeball icon on the track header.
Open Audio track, clip Properties, Video Tab, Track = None, then Audio Tab, select alternate Audio Track. Drag source clip to audio track.
OBS help tip… Add a 3rd track, and put your Mic + Desktop Audio on that track.
In OBS I always have Audio Track 1 as Mic+Desktop.
This is the preferred way, and there is no need to change the video track to none as using an audio track takes care of that.
I see that the consultation is already solved.
This is the advantage of different time zones.
There’s always someone to the rescue. 
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