Apple deprecated QuickTime as a system driver for time based media back in 2013 in favor of AV Foundation Frameworks. Most players (including VLC Player, Handbrake and most any other player application out there) require QuickTime in order to play the wide range of formats and CODECs that were supported by QuickTime.
There's a very short list of CODECs that AV Foundation Frameworks fully supports: Apple ProRes, H264 and as of macOS High Sierra H265. A short list is supported for playback only (Photo-JPEG, MPEG2, DV-NTSC, DVCPro, and a handful of others).
The tricky part about the rollout of AV Foundation Frameworks is that the file format is still a QuickTime movie file (.mov).
Adobe announced application level support for some of the QuickTime CODECs (like Animation) back in May.
So, what am I saying here? It's entreily possible that you may need to roll your OS back to a prior version so that you can be working with the full support of QuickTime at the OS level in order to play and/or convert your movie file.
I highly recommend anyone using QuickTime who may have not yet worked out how to continue their workflow without QuickTime working at the OS level watch the following video:
Moving to AV Kit and AV Foundation - WWDC 2013 - Videos - Apple Developer
And perhaps read the PDF that went with that presentation here:
http://devstreaming.apple.com/videos/wwdc/2013/606xdx2xbp31zp28fdov8p0b6d/606/606.pdf
Scroll to page 29 to see the CODECs no longer supported. You can also include any 3rd party QuickTime based CODECs as unsupported as well.
If you're running the macOS, it's very easy to tell if your files won't play without the QuickTime system drivers installed: If QuickTime Player X shows "Converting..." when you open a movie file, that's QTMovieModernizer (a component of QuickTime) converting your files for you. Be sure to save the converted file if you want to be able to open and play your video when QuickTime is gone. (And, as of last week with the release of High Sierra, it's gone).
