I am trying to enable extended configs but every time I launch the game it re-generates the config file, setting the value to false, and extended configs are not generated.

Neoforge version: 21.1.172
Relics version: 0.10.7.5

OS: Linux mint 22.1 x86_64
Ryzen 5 2600, RTX 2060

Does the issue recur if you first exit the game, then change the field in the config and save the file, and only then launch the game?

Yes, and then when the game is launched again it gets overwritten