All In

For each clue in the top section, the letter at a certain position in each word has been replaced. For example, in "Hove hhythmically hide ho hide", the first letter of every word has been replaced by H. We can figure out what the words should have been and solve the repaired clues and make the same modification to the answer:

Given Clue	Repaired Clue	Answer	Modified Answer	Replaced Letter
Appll peellr, for examlle (5)	Apple peeler, for example	PARER	PAREL	R
Bgnites, berhaps bith blint bnd binder (6)	Ignites, perhaps with flint and tinder	SPARKS	BPARKS	S
Codsbreaker, mayse (13)	Codebreaker, maybe	CRYPTOGRAPHER	CRYSTOGRAPHER	P
Cot woth ao aoe, loke a lomberjack (3)	Cut with an axe, like a lumberjack	HEW	HOW	E
Fwakes ow pwecipitation (4)	Flakes of precipitation	SNOW	SWOW	N
Ganaging gespite gifficulties (6)	Managing despite difficulties	COPING	GOPING	C
Hove hhythmically hide ho hide (4)	Move rhythmically side to side	SWAY	HWAY	S
Lestaurant lr lther llace lo lonsume lood (6)	Restaurant or other place to consume food	EATERY	LATERY	E
Uaper caass, naarly nability (6)	Upper class, nearly nobility	GENTRY	GANTRY	E
Wotd a ghtst mitht ust to sttrtle soteone (3)	Word a ghost might use to startle someone	BOO	BOT	O

Now, the bottom clues can all be solved to yield a word which is a modified answer from above with ALL inserted (fitting with the title of the puzzle):

Clue	Answer	Corresponding Modified Answer (from above)	Corresponding Replaced Letter (from above)
Corridor	HALLWAY	HWAY	S
One who might study certain lattices	CRYSTALLOGRAPHER	CRYSTOGRAPHER	P
Consecrate	HALLOW	HOW	E
Analogous	PARALLEL	PAREL	R
Chivalrous behavior	GALLANTRY	GANTRY	E
Moving quickly	GALLOPING	GOPING	C
It goes in a box to be counted	BALLOT	BOT	O
To the side	LATERALLY	LATERY	E
Bird	SWALLOW	SWOW	N
Where certain games are played	BALLPARKS	BPARKS	S

Reading these letters yields the phrase SPERE COENS, which has also been modified like the top clues: the third letter of each word has been replace by E. Figuring out what the words should have been yields the repaired clue phrase SPARE COINS, which yields CHANGE. Modifying this by making the third letter E yields CHENGE, and finally inserting ALL yields the final answer CHALLENGE.