Hi,
I’m definitely not sure about what could cause such an issue, it seems more like an engine bug.
I’ve researched some answers and read some things that could help you here: Godot @export var is Nil in _ready function and https://www.reddit.com/r/godot/comments/1b90b2y/export_variable_keeps_getting_set_to_null/
One question though, how is your main menu scene instantiated? I suppose you’re placing it by hand or instantiating the main_menu.tscn file, right? Because such issues can happen if you create instances in code using the new keyword. Definitely doesn’t look like something you’re doing, but I just want to make sure of that.