>"lost" media that 100% exists in storage but will likely never be available to the public
Evangelion 3.0 theatrical dub before Khara made them redo it and took control of all future English scripts.
>actual lost media that most likely does not exist in any condition anymore
TV broadcast of Machinal starring Donald Pleasance as the husband. When they released the series on DVD there were a handful of episodes they couldn't locate the tapes of and that was among the missing ones. It's well-known British TV studios would save money by taping over the masters for shows that had already been broadcast (reason some old Doctor Who is missing), so that's my guess as to what happened.
Also Tod Browning's original cut of Freaks.