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This is a letters-latent cryptic crossword: an equal number of Across and Down clues have one extra letter in the wordplay that should be removed and noted down. These letters spell out a phrase which, interpreted correctly, indicate four words that the solver should find and highlight in the finished grid. Two Across clues and two Down clues have an extra word that should be removed before solving; these four words should indicate what the solver is to write in the sub-cells starting at $3$D and moving across. If extra help is needed it can be found nearby. All other clues are normal.

All words except proper nouns can be found in Chambers Dictionary. One word, unusually, has no accent in British English but has retained the accent in American English; the British version is preferred for this crossword.

Across:
1.   Wrestling tournament remains in box office (5)
5.   Military ruler's kind of wedding? (6)
11.  Autumn bake I ate later to repay in kind (9)
13.  Priest changing direction of line-up (4)
14.  Not sober (i.e. sober after a fashion) (7)
15.  Trap oddball (3)
16.  Egyptian spirit (at the time) is lighter than Hydrogen ion (4)
18.  German border river -- "Border A" lacking support (4)
19.  Leaves Inverness' swirling gases (4)
20.  Winter apples from Cyprus set standard (7)
21.  A fib (French one) is repugnant (5)
24.  Treat as an injury and put broken bone back in place (5)
26.  Wood between cargo leads to damp under new nets aboard _Greek Empress_ (7)
29.  Lady Lovelace (mechanical engineer) knight's wife (4)
31.  To explain "magic" untie ends at any time (4)
32.  Leone's little western post office company (4)
33.  I put drink before Romanian bread (3)
34.  Calling earnestly for e.g. Quahog social worker... (7)
36.  ...Welsh chap unsettled Lucan (4)
37.  Various dead -- no sign of Americans. Inoculate against smallpox!  (9)
38.  Lyric writers elaborate: it's dosh (6)
39.  Skinner dismisses answer from one on a plane (5)

Down:
1.   Empty boasting: bishop ruined a good cigar (11)
2.   Lofty melody that is written in Latin (6)*
3.   Walthamstow necklace incorporates gem (5)
4.   Spring eagles for example; they advocate hostility (5)
5.   Blood relation up-ended bias (3)
6.   Scottish intellect endures holding gas (5)
7.   Torn-down zoo: site is unoccupied (6)
8.   Germanium oxygen einsteinium takes in initial dopant producing 3s with crystal cavities (6)
9.   Mother's sister takes pinch of salt with drug (it's not confirmed) (5)
10.  Entire resin fermented for Rhine wine (11)
12.  Get to know forerunners of linguistics education and rudiments of noology (5)
17.  Live through loss of English from old tongue disease (5)
22.  Intaglio grooves: essentially plain cavities (6)
23.  Ernie smears oddly fundamental fluids! (6)
24.  Short clergyman opens Apocrypha to right page (5)
25.  Popular summer uproar: last of the plum wine you might see (6)
27.  Race and be ahead without acceleration and lacking direction (5)
28.  A hidden danger rising up separately (5)
29.  Factotum is dead on arrival, left in middle of rurality (2-3)
30.  Quell everyone Yau confused (5)
35.  Friendly Swedish goblin brings up moral offence (3)

* Originally this was "Lofty melody, for instance, written in Latin" but Deusovi correctly pointed out that I'd messed the clue up.

[Note: Google Translate is less reliable than Google for some things.]

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  • $\begingroup$ I think I've figured out the theme, but I still don't know what the extra letters mean... might post an answer soon if I can't get the last few clues. $\endgroup$
    – Deusovi
    Jul 16 '20 at 16:55
  • $\begingroup$ The Note might be a hint :) $\endgroup$
    – user40528
    Jul 16 '20 at 16:56
  • $\begingroup$ Don't think I have enough to use the note, unfortunately. The string I have just looks like nonsense at the moment. $\endgroup$
    – Deusovi
    Jul 16 '20 at 17:01
  • $\begingroup$ @Deusovi It's not in English, and the string splits as (4,9,4,1,5) which together with google should give you the bit you need. The language clues were intended to be from the small letters in the grid, but maybe I've been a bit too obscure? Do you think I should have specified the string split as part of the preamble? $\endgroup$
    – user40528
    Jul 16 '20 at 17:06
  • $\begingroup$ Yeah, I figured out what the six letters at the location of the small grid letters refer to. I assume the "nearby" help refers to 1A and 5A sharing a certain property. Beyond that I'm stuck. I only have 19 letters, some of which I'm not sure of, and... wait, shouldn't there be an even number of letters, because of the "equal number of Across and Down clues"? 4+9+1+4+5 is odd. $\endgroup$
    – Deusovi
    Jul 16 '20 at 17:08
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The grid:

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Clue explanations:

2

Bold clues are unsolved. Red bold shows the four words that are to be removed. Blue bold is words that look useless as I currently understand the clues, but don't seem to be part of the puzzle gimmick.

The theme, as I currently understand it,

relates to the current time in the middle of summer. The letters with the small squares spell SHOSHO; shōsho is one of the 24 solar terms of the East Asian calendar, taking place in around the middle half of July. It is expressed in Japanese, which is potentially hinted by "basho" and "shogun" -- both of the entries that contribute three letters to it -- being Japanese words.

The extra letters spell TAKA SUNAWACHI WAZA O NARAU -- in Japanese, "[When the] hawks learn to fly". This is one of the three "microsesasons" that the season of shōsho is divided into. The words HAWKS LEARN TO FLY all appear in the grid (some as parts of other words).

I'm not sure what to write in the small boxes. None of the given phrases seem to have six characters in Japanese (either as hiragana or kanji), nor do the words "season" or "summer" in Japanese. The intended answer could be to write SEASON or SUMMER in there, but I'm not sure what that would do specifically.

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  • $\begingroup$ (Also, I assume the "accent" comment refers to 1A. Will update when I edit this answer with more clue explanations.) $\endgroup$
    – Deusovi
    Jul 16 '20 at 17:16
  • $\begingroup$ Grid answers are all correct, and you've identified the theme :) The words you've highlighted in blue contribute letters to the phrase you need to find, which is why they seem out of place, I think :) $\endgroup$
    – user40528
    Jul 16 '20 at 19:21
  • $\begingroup$ 15A is double def, but one word is longer than the other. 24 is also double def, but one word longer than the other again. Both of those will give you extra letters. 2D is the right answer but the wrong extra letter. I think that if you take the extra letter from 24D and google the last three words that will help you enormously :) $\endgroup$
    – user40528
    Jul 16 '20 at 19:28
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    $\begingroup$ @postmortes For 2D, EG is "for instance"; IE is "that is". I also had been under the impression that there wouldn't be any pieces that just gave the extra letter, without contributing to the wordplay in any other way -- that's generally not done with this gimmick in my experience. $\endgroup$
    – Deusovi
    Jul 16 '20 at 20:50
  • $\begingroup$ You are completely right about 2D and I'm sorry; staring at the clues for too long makes some things too easy to miss :( I take your point about the wordplay: I guess it's unfair to the solver. Thank-you for taking the time to persevere with this, and I'm sincerely sorry that you've had such a bad solving experience. $\endgroup$
    – user40528
    Jul 17 '20 at 5:14

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