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I usually do everything from CLI.
Are you wanting to re-encode it to a different codec or just change the container from mkv to mp4?
To remux the file (change the container format), you can simply do:
# The -f mp4 is technically optional as it can deduce it from the extension, but I like to be explicit
ffmpeg -i file.mkv -f mp4 file.mp4
That should go very fast as it's just copying the streams as-is into a new container.
If you want to re-encode it to a different codec, then you'll need to use a more complex ffmpeg command.
CLI can be scary, but this is such a simple command to run. It should not be too intimidating.
If someone really needs a GUI, I believe VLC's file conversion capability is basically just running an FFMPEG command like that in the background.

I am not sure file formats are like religions. I mean, some of them are cross compatible. Totally unlike religion.
According to: https://help.archive.org/help/movies-and-videos-a-basic-guide/
What encoding specifications are best for .mp4 files?
For your original mp4 to work in the online player we currently require the file to have:
audio: aac
video: h.264
moov atom: front
pixel format: yuv420p
FFS, they're not even on h.265 yet. Ugh.
H.265 requires hardware decoding
Not necessarily, but it does require a lot of computing power to decode in real time.
But good point, h.265 encoded video is not accessible for much of the world.
You can do it with ffmpeg (CLI) and I can give you the incantation for that if you want, but the IA's transcoding pipeline should really do it automatically and I'm surprised if it doesn't do it already. I wonder if it's supposed to and something is going wrong. I assume you used .mkv extension and still got that error. So that sounds like a bug. Otherwise, try renaming the file and re-uploading.
If it's a bug, you could try contacting the IA and asking what's up. They do read the emails they get, though obviously a software fix is likely to take a while if they pursue it. https://archive.org/about/contact