make an overlay, for example create a script in /usr/share/batocera/configgen/scripts/ (to be executed BEFORE launching emu) which add the file back in PCSX2 system folder then save it with command batocera-save-overlay. you will be safe until next system update (just re-do the trick if it’s still not fixed). Check here for more details.
This is what I made to keep cemu and rpcs3 up-2-date on my RIG.
It’s the main downside of batocera, it act like a firmware, each system modification is removed at reboot. While I kinda understand why they done it that way, it would be far better to have a normal writable system, at least for PC/NUC.