Stroke_Papy Can you write some more details, please? Does LE audio work with a different firmware? I don't understand what you wrote.
The RPi firmware is written to the chip, so it stays active when you switch to another OS / microSD. config.txt / guisettings.xml are not relevant for this part.
If the firmware is the issue, you have to find a version that works with all your OS'es. Maybe switch from Retropi to Lakka, if Retropi needs incompatible firmware.