I've been trying to write up some questions to understand your problem better, but I can't think of what could be the issue.
It seems like some project setting would be the only difference between your project and a clean project... not sure how you would compare, but do you remember changing any project setting in the project that isn't working?
One thing that has helped me with an unrelated issue is clearing the project cache... on windows it's in
%appdata%/roaming/godot/projects/yourProjectName... or something like that... and in your actual project folder, deleting the .import folder and all the .import files... I can't imagine what could this could change for you, but as a last resort