With a handful of exceptions, almost every cutscene audio file has slight differences from the final game, let that be audio balancing, Black Doom's missing warped voice or missing sound effects.
The following cutscene audio files are byte-by-byte identical to the final game:
The final version trims the voice clip to remove the "and have thoroughly disappointed me." line. Do note that Doom's Eye's line "You have failed your mission." goes unused in the final.
cty03_e16_kn.adx
Knuckles
"No!" was completely removed in the final.
cty03_m05_bd.adx
Doom's Eye
"Now, let this city fall!" was removed in the final.
cty03_m20_kn.adx
Knuckles
"That's all of them!" was removed in the final.
ark01_m10_mr.adx
The Doom
Maria
"I'm so relieved!" was removed in the final.
can02_m06_bd.adx
Sky Troops
Doom's Eye
"Let this be an example to any who seek to defy us."
"Well Done, Shadow..."
The line was completely redone in the final, and an outtake can noticeably be heard here. This wouldn't be the last time where an outtake was left in by accident.
can02_m06_eg.adx
Dr. Eggman
"There!" was removed in the final.
elc02_m04_es.adx
Mad Matrix
Espio
"You cannot fathom how so." was removed in the final.
elc02_m05_bd.adx
Doom's Eye
"Now, let's go!" was removed in the final.
all01_n05_rg.adx
Death Ruins
Rouge
There's a long pause at the beginning, and "Great job!" was removed in the final.
ark02_m05_bd.adx
The ARK
Doom's Eye
"Now" was removed in the final.
all01_n05_tl.adx
Air Fleet
Tails
"All right!" was removed in the final.
bas01_m04_bd.adx
Doom's Eye
"The president has been terminated." was removed in the final.
ark03_m14_bd.adx
Space Gadget
"Hmph!" was removed in the final.
all01_n05_mr.adx
Lost Impact
Maria
"That's all of them!" was removed in the final.
bas02_m05_bd.adx
GUN Fortress
Doom's Eye
"Well done! Final victory is now ours."
"Well done, Shadow..."
The line was almost completely redone in the final.
bas03_m05_eg.adx
Lava Shelter
Dr. Eggman
"Shadow!" was removed in the final.
Many characters also state that pressing the X button would allow the player to use Chaos Control, but this isn't true, as Y is the one used in the final Xbox version.
Filename
Character
Prototype
Final
all02_h03xb_bd
Shadow
all02_h03xb_bd
Doom's Eye
all02_h03xb_sn
Sonic
all02_h03xb_sd
Rouge
all02_h03xb_kn
Knuckles
all02_h03xb_eg
Dr. Eggman
Sonic's voice clips from Space Gadget are correctly prefixed as sn instead of sd like in the final.
Almost Dead by Powerman 5000 and Never Turn Back don't exist in the game at this point, their filenames (sng_vox02.adx and sng_vox06.adx, respectively) are occupied by an unlooped full version of I Am... All of Me that doesn't exist in the final game.
Filename
Music/Song
Prototype
Final
Notes
sng_vox03.adx
Waking Up
Instrumental only, different mixing and some parts are different.
sng_vox04.adx
Broken/The Chosen One
This song was originally supposed to play in the semi-Hero ending, but didn't make the cut because Jun Senoue couldn't track one of the band's members. It would eventually be reworked into The Chosen One.
sng_vox05.adx
All Hail Shadow
Different instrumentation, different lyrics in some parts, and different vocal performance. Most likely a demo recording.