There are only 3 sounds that are used for the Cyclops.
The AC-Four Ship Engine.wav and AC-Four_hyd.wav are the same.
The only other sound is Vapor Siaj.wav.
Defined in the dsd file as Ship.Liberty.Shipwake
That may be the one you want to remove from the dsd file.

No, no, I'm trying to remove the actual effect of bubbles emitted from the propellers as they spin. I've removed all the sounds I wanted, and even made the sounds the ship emits quieter.

That's the helix thing in the particals.dat I believe.
But it's a hard coded thing so if you change the effect?
All props in-Game would be affected.

You could create an animation of a prop so it spins.
Then do away with the standard props as was done for things like Iceburgs and such.

...gah! I don't know how to do this... my hex editing skills are questionable at best.

S3D will allow you to do all you would need to do.
:yep:

Just add the aircraft prop animation to the props of the Cyclops and adjust the speed to your likeing as a start.
Add a dummy prop like what was done for the Whale and point the sim file to it.
:D