From the link I posted:
John Beck's Monadicity Theorem is cited in "many sources" but a manuscript has been found and "The proof is reproduced for instance in (MacLane, p. 147-150, Riehl 2017, 5/5/)".
Fred Linton cites Michael Barr for a "Universal property of the Kleisli construction" and no copy has been found.
I don't know enough about the subject to say how difficult these proofs would be to recreate or whether they exist elsewhere, but these definitely seem to be specific theorems.
I'd like to see a specific theorem in any field that was once proven and accepted but all existing proofs have been lost. That would be extremely tantalizing