I noticed that all of the newer episodes are playing back as VP9 rather than MP4. Have you done anything special to achieve this?
Wikipedia says that VP9 :
VP9 is an open and royalty free[3] video compression standard being developed by Google. VP9 had earlier development names of Next Gen Open Video (NGOV) and VP-Next. VP9 is a successor to VP8. Chromium, Chrome, Firefox, and Opera support playing VP9 video format in the HTML5 video tag.
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So YT/Google must have decided that it was time to change to their new format, Maybe they had to start to pay royalties for using the MP4 format?