I have read about a similar issue in the forum, and the solution was to install the pulseaudio driver.
Before you try, back up your setup!

sudo apt install pulseaudio pulseaudio-utils

OK so this worked:

I added the following to runcommand-onlaunch.sh

rm /opt/retropie/configs/ps2/Config/cache/vulkan_pipelines.bin && rm /opt/retropie/configs/ps2/Config/cache/vulkan_shaders.bin && rm /opt/retropie/configs/ps2/Config/cache/vulkan_shaders.idx

It did not appear to like them on separate lines. Now when a game launches, it deletes those three files, and if I'm loading a PS2 game with AetherSX2 it re-creates them once the game loads, but then deletes them before the next game.

So this way those files never get bloated and not hog down any other games.