With T63805 deployed, new video uploads will be producing VP9/Opus WebM transcodes instead of the old VP8/Vorbis configuration. We still have to back-fill in the old files for consistency; this can be done with requeueTranscodes.php.
On mwmain1001, run something like:
mwscript extensions/TimedMediaHandler/maintenance/requeueTranscodes.php --wiki=commonswiki --throttle --video --missing
in a tmux session. This will go through all video files on the wiki and for any missing transcodes in the currently defined set (VP9) it'll run them. The --throttle option is important to keep from flooding the queue with thousands of files.
I'll start running this shortly.