->Transitions->

Question

Here is a crossword to solve; the yellow squares hold a relevant word.
Online tools will be useful/needed.

partial text transcription:

> ACROSS
> 1. Distance to the Star Wars’ g                            ?
> 3. Bacon soBAABBBAAAAAAABAAABAA
> 10. A possJAPC RBQC DKN SGC CREKFJRH SGBS 0BT KRP3 VTCF JR 6WB BRF YZB
> 12. Mistakes flagged for corr                           
> 15. Wonder at;                                      
> 18. Fin5   3 15 6 6 5 5
> 21. Downy se
> 23. What those using 24D’s cipher mig….  -     .-..   .-  -.-.  -.-  
> 25. Makes difficult to see, like a fence, PAEHPRS
> 26. That which is coming int---    -…  .  ..  -.  --.
> 27. Items used in 4D’
> 29. Chaos’ op
> 30. Things in a col .-..  .  -.-.  -  ..  ---  -.
> 32. Forerunner
> 33. Country on Namibia’s northe 
> 35. A posTJAPC RBQC DKN SGC CREKFJRH SGBS 0BT KRP3 VTCF JR 6WB BRF YZB 
> 42. Apollo-13 eATVARRE?
> 43. 504, in 16D’F AHZRENYF

> DOWN
> 1. Nine, in 16D’ 
> 2. A small, squali 
> 3. Color made by scrambling LLOEYW NAD ORNBW
> 4. Extrasensory perception, foAr  KOPArCa
> 5. Aegean, ELPMAXE ROF
> 6. Columbus’ ship, ATNAS HTIW
> 7. Container for mixed USTN RO OOIECKS
> 8. OpPOSITE OF 13D 
> 9. Color made by scrambling LLOEYW NAD ORNBW
> 11. Large box 4 HAULING 1DERFUL THINGS, LOL 
> 13. Very s --  .-  .-..  .-.. 
> 14. Arrangements of pentom ..  -.  ---  .  ...
> 15. Like-minded bod 
> 16. Complex and involved, like thiXIX  XVI XXI XXVI XXVI XII V
> 17. Self-m  
> 19. Burner use 
> 20. Add into a collection, as in SQL, or add 3 rails to a FEECN
> 22. Best or moFG SNIBENOYR
> 23. Prisoner’s view; prison .  …..  …. ..  ‘ ….  ...    .  ….  .  …..  ….  …  ..  ….  ….  ..  .  …..?
> 24. Peninsula known for it 
> 28. Inclin 
> 31. Terms of Servi  
> 32. Thirteen snBJ ZBAFGREF?
> 34. Two-legTRQ PERNGHER
> 35. Tolkien ERUTAERC EERT
> 36. ___thermal enBArNMn
> 37. AnsweR TO 7D
> 38. Bone taken MADA MORF
> 39. Hazy LondON FEATURE
> 40. Tangle or bash intL Z GSRXP NZHH LI IFT
> 41. In 4D’s cipher, it’s num2 5 18   20 23 5 14 20 25

Answer 1

Obviously, the back halves of the clues have all been encoded somehow.

Several clues hide references to their encodings inside them. Below, I've bolded the decoded parts of the clue, and underlined any hints towards the cipher.




There are some nonstandard ciphers in there:
"remove verticals" isn't really a cipher, because it's not reversible. Those clues have you remove all vertical bars from them.
"anagram" is similarly not a cipher.
"sideways" just has all letters tilted on their sides. "identity" is the transformation that does nothing at all - the plaintext is the same as the ciphertext.

And of course, there's the one used in 10A and 35A, which look to be the same clue. It doesn't appear to be a well-known cipher, but you can bruteforce it as a cryptogram to get the clue:

10. A possible name for the encoding that was only used in 10A and 35A

Filling the grid

Some entries don't fit in the grid in the natural way. So what do you do?
It turns out you can only fill the grid by encoding each answer in its corresponding clue's cipher. The result of this is shown here:


To fill 10A and 35A, you need to use crossing letters (converting them back before trying to fill in the blanks). 10A turns out to be SUBSTITUTION CIPHER, and 35A turns out to be STRAIGHTS AND CURVES. The cipher for those clues is generated by lining up all the characters written with only straight lines, and all the ones that have a curved line somewhere:
AEFHIKLMNTVWXYZ147
BCDGJOPQRSU0235689

Then, each letter is replaced with its partner in the above two lines. The highlighted letters, when decoded according to the ciphers from their Across clues, spell the answer: ENCRYPTION.

Answer 2

I haven't worked out how to fill out the whole grid yet, but here's what I have for all of the decoded clues, if it helps save anyone some time:

Across:

1 DISTANCE TO THE STAR WARS GALAXY
3 BACON SOURCE
10 A POSSIBLE NAME FOR THE ENCODING THAT WAS ONLY USED IN 10A AND 35A
12 MISTAKES FLAGGED FOR CORRECTION
15 WONDER AT; COMICS PUBLISHER
18 FINE COFFEE
21 DOWNY SEA DUCK
23 WHAT THOSE USING 24D'S CIPHER MIGHT LACK
25 MAKES DIFFICULT TO SEE, LIKE A FENCE, PERHAPS
26 THAT WHICH IS COMING INTO BEING
27 ITEMS USED IN 4D'S CIPHER
29 CHAOS' OPPOSITE
30 THINGS IN A COLLECTION
32 FORERUNNERS OF EFFECTS
33 COUNTRY ON NAMIBIA'S NORTHERN SIDE
35 A POSSIBLE NAME FOR THE ENCODING THAT WAS ONLY USED IN 10A AND 35A
42 APOLLO-13 ENGINEER?
43 504 IN 16D'S NUMERALS

Down:

1 NINE, IN 16D'S NUMERALS
2 A SMALL SQUALID DWELLING
3 COLOR MADE BY SCRAMBLING YELLOW AND BROWN
4 EXTRASENSORY PERCEPTION, FOR SHORT
5 AEGEAN, FOR EXAMPLE
6 COLUMBUS' SHIP, WITH SANTA
7 CONTAINER FOR MIXED NUTS OR COOKIES
8 OPPOSITE OF 13D
9 COLOR MADE BY SCRAMBLING YELLOW AND BROWN
11 LARGE BOX FOR HAULING WONDERFUL THINGS LOL
13 VERY SMALL
14 ARRANGEMENTS OF PENTOMINOES
15 LIKE-MINDED BODY OF PEOPLE
16 COMPLEX AND INVOLVED, LIKE THIS PUZZLE
17 SELF-MEASUREMENT
19 BURNER USED TO HEAT 27A
20 ADD INTO A COLLECTION, AS IN SQL, OR ADD 3 RAILS TO A FENCE
22 BEST OR MOST FAVORABLE
23 PRISONER'S VIEW; PRISONER'S DESIRE
24 PENINSULA KNOWN FOR ITS NIGHTS
28 INCLINED PLANE
31 TERMS OF SERVICE, FOR SHORT
32 THIRTEEN SNOW MONSTERS?
34 TWO-LEGGED CREATURE
35 TOLKIEN TREE CREATURE
36 ___THERMAL ENERGY
37 ANSWER TO 7D
38 BONE TAKEN FROM ADAM
39 HAZY LONDON FEATURE
40 TANGLE OR BASH INTO A THICK MASS OR RUG
41 IN 4D'S CIPHER, ITS NUMBER TWENTY