Dropping this here since its better than just a comment on the forum thread.

After removing many mods, and stumbling upon the author's comment regarding sound vanishing with hyperwarm, I too came to the conclusion that the source of the issue ive been battling perhaps has been timewarp's hyperwarm.

Unsure EXACTLY what triggers it, but its either dying / getting an explosion or detaching a stage while hyperwarped, or simply over time, that it causes the Vessel's sound effects to simply vanish, so you hear just the air, blowing if on kerbin, and silence in space.
Music still plays, but the Ship engine, RCS and gear sound effects are gone until you restart the game.

Affecting every vessel you pilot once the bug triggers, requiring a restart to fix and hear the sound effects again.

Timecontrol mod is love, but losing sound effects is sad

Is there a fix for this?

Addition:

It seems that the time warp in 1.12 messes with some distance sound calculation. Which basically makes the game think the engine sounds are farther than what they normally (pre hyperwarp) are. It thinks they are way back farther behind the camera, instead of infront of us, coming from the engines. It decides to play the sound distant from it.

Eventually of course it silences it entirely and kills it on any vessel, until the game is restarted. Hyper warp initiates all.