Yes, this can happen when you switch from Windows to Linux. I think it has something to do with the line endings. I tried to convert the files manually, but that did not seem to fix it. If I recall correctly, what I did was open the main project file and removed the line that specified the main scene. This allowed me to load the project in Godot. Then I simply selected that same scene as the main scene and it rewrote the project file. The file looks exactly the same if you look in the text editor, but the binary is different. Maybe you can edit it a hex editor but I never tried.
