I am wondering about the jot messenger app and the albums app. These two apps allow video uploads. Does the "bx_videos_video_mp4" and "bx_videos_video_webm" take care of those videos too? If so, then the issue is solved.
There are videos in other modules which have own record in sys_transcoder_filters table, so it needs to be updated separately. You can have a look at all records where filter field equals to Webm and Mp4 and make similar change.
