Oops! All Acros--

Question

^{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.

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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)

Answer 1

Nearly complete answer. I'm missing what I think is the last step.

The grid:

    E X T R A C R E D I T
    T R E E M A U R I D U
    A A M F O R D U S E R
    T Y P E K E E P S A N
    A W O R S T S T E N O
    N A C R E I M P R O V
    E J E C T S O U T R E
    W A N E S I G L O O R
    L E T L A D S O K R A
    E T A L B O W S A E K
    A U U I U L A E P E E
    F I R S T S T R I K E

The clues:

1. Nearly root out replica with right doctor giving bonus points (5, 6)
    — EXTRACT = EXTRAC(t) + R + EDIT
12. Maybe palm off – that's way out of bounds (4)
    — TREE = (s)TREE(t)
13. Waterfront crossing dedicated to daughter (4)
    — FOR = FOR + D
14. American entrepreneur is gutted by vindictive client (4)
    — USER = US + E(ntrepreneu)R
15. Inferior group is expanded 50%, secretly (4)
    — TYPE = (fif)TY PE(rcent)
16. Honor contract of revolutionary peer (4)
    — KEEP = PEEK<
18. Most incompetent oligarch is a banger, I hear (5)
    — WORST, homophone of WURST
20. Fast writer composed legible notes (5)
    — STENO = NOTES*
21. Pearl's filming new unit of Illuminati territory (5)
    — NACRE = N + ACRE
23. Polish version mostly unplanned (6)
    — IMPROV = IMPROV(e)
24. Throws out heel of shoe, airplanes, cans, club, &c (6)
    — EJECTS = (sho)E + C in JE.TS
25. Tout video recorder components as "extraordinary" (5)
    — OUTRE = (t)OUT RE(crorder)
26. Fades away, as new malformed idiom (5)
    — WANES = (AS NEW)*
28. White House app created by big loon on the inside (5)
    — IGLOO = (b)IG LOO(n)
32. Fellows praise introduction of "natural spirituality", taking off uniform (4)
    — LADS = LA(u)D + S(prituality)
35. Vegetable is despicable (but acceptable before treat, regularly) (4)
    — OKRA = OK + (t)R(e)A(t)
38. Reflecting over viewpoint for additional contributors (2, 2)
    — ET AL = LATE<
39. Shows respect and declines invite (4)
    — BOWS (ddef.)
40. Steel edged program elements elicit inter– faces (4)
    — EPEE = E(dged) P(rogram) E(lements) E(licit)
41. Right to enter Duke's infamous three-wheeler, being a third of the way out (5, 6)
    — FIRST STRIKE = R in FI.ST'S + TRIKE

The two unclued down entries ...

... at 11 and 17 spell: Turn over a new leaf.

The first characters ...

... of the extra words, crossed out in the clues above, spell, Row VI & Col IV and VIII. The letters at these positions spell: R.I.P. or maybe rip.

The last characters ...

... of the extra words spell: After the incomplete –s. The preamble explicitly mentions characters, not letters. The extra word in 40 across is "inter–", making the last character a dash. The preample also mentions "repl[acing ...] characters". I guess that we need to replace the dash with the message found by the first characters, "RIP", so: After the incomplete rips.

This obviously refers to what would be on the torn off part of the page. An "incomplete rip" is one where the tear goes through a letter. This occurs in nine clues:

     3.   Worke R ... [TEMP in TEMPO]
     5.    Bers E rk ... [AMOK]
     7.   Uncul T ured ... [RUDE]
     9.    Reve R sed ... [(TRESS + DI)<]
    19.    Plac E s ... [SETS]
    28.   We he A r ... [homophone indicator for IDLES?]
    33.   Inver T ed ... [TUBA<]
    34.   Strik E ... [SWAT]
    36. beheade D ... [common indicator; REEK]

So ...

... the capital letter is the one that, in the words of the preample, "should be there". These letters spell out retreated.

This could be "how the hosts [reacted | behaved | ...].

Is this the end?

Hm. I don't know. There's still the question how things could be put back to normal, as Gareth sugests, by "turning over a new leaf". And I don't quite see what the "discovery" mentioned in the preamble might be.

Thanks to ...

... Gareth for corrections, observations and discussion and to Deusovi for the hints and, of course, for a super puzzle.