Ran into this last night on PC, I got the secret level elevator to spawn on stage 4 of fixed mode, had a Hyperfunk Zone spawn while there, and upon leaving HFZ, all SFX were muted.
Unsure if there were other variables in play. Was Toejam (not oldskool), got to the second stage of HFZ. Game was online and open to public but no one joined. :'(
I saw a ticket that said the secret level losing music was fixed, but this was just SFX.
This happens when exiting the hyperfunk zone.
I lost all SFX on secret level while music continued. It was fine once I left.
This happens to me very reliably on Switch.
Happened the other way around to me on Steam. When we left HFZ the music was the only sound still around, and the sound effects all came back after leaving the secret level.