This puzzle was originally formatted as a PDF; the puzzle PDF is available on Dropbox. A screenshot of the PDF is available below. This puzzle is an entry in Fortnightly Topic Challenge 46, "Tales from the Cryptic".
This is a sequel to Not Bluebeard's Castle, which reveals a certain set of works to be the theme of both itself and this puzzle. No knowledge of the works in question is necessary to solve this puzzle. It is highly recommended (though not necessary) that you solve that puzzle before this one.
Transcript of instructions and Across clues:
Oh no! It looks like part of the page The two unclued Down entries tell y normal. The Across clues each have an extr clue. The first characters of these message. The last characters (repl characters) tell you a location on t nine letters that should be there sp discovery, as well as how the hosts Across 1. Nearly root out replica with right doctor giving bonus points (5, 6) 12. Maybe palm off — that's way out of bounds (4) 13. Waterfront crossing dedicated to daughter (4) 14. American entrepreneur is gutted by vindictive client (4) 15. Inferior group is expanded 50%, secretly (4) 16. Honor contract of revolutionary peer (4) 18. Most incompetent oligarch is a banger, I hear (5) 20. Fast writer composed legible notes (5) 21. Pearl's filming new unit of Illuminati territory (5) 23. Polish version mostly unplanned (6) 24. Throws out heel of shoe, airplanes, cans, club, &c (6) 25. Tout video recorder components as "extraordinary" (5) 26. Fades away, as new malformed idiom (5) 28. White House app created by big loon on the inside (5) 32. Fellows praise introduction of "natural spirituality", taking off uniform (4) 35. Vegetable is despicable (but acceptable before treat, regularly) (4) 38. Reflecting over viewpoint for additional contributors (2, 2) 39. Shows respect and declines invite (4) 40. Steel edged program elements elicit inter– faces (4) 41. Right to enter Duke's infamous three-wheeler, being a third of the way out (5, 6)