So, I've been trying to figure out a solution for the D.Tube format issue. There is still no way to actually remove the invalid video (though that should be considered a bug: Only allow h.264/h.265/WEBM/OGG formats because otherwise video will not play in HTML5 player).
I first tried to convert the video using HandBrake. This has been a massive failure, as HandBrake won't properly sync the audio and video. What was 43 minutes is now 72, although the audio is still the original 43. And yes, I tried selecting the "Same as Source" for bandwidth, and same problem.
Well, after a few failures, I went into my YouTube, and found I was able to download the mp4 directly from my uploads. So, YouTube already converted it for me. This is going to make things a lot easier in the future. I'm uploading the mp4 now, so there shouldn't be any issue.