Hmmm... Sounds strange, and is potentially some sort of project management bug in Godot. A screenshot of what you're seeing might be nice.
And, you can't delete it because that line doesn't have that option (the trash can), or it has the option but it doesn't work, or ??
Anyway, if you can't clean it up through the interface, you can probably do it manually, by hand-editing the
project.godot file in the root of your project folder.
Note, while I'm relatively confident this is safe, I'd suggest you have a backup before hand editing the project file. Better yet, hopefully you're using Git or some other form of SCM that makes this 100% safe. Also, know that I'm no expert here (so continue at your own risk) but if it were me, I'd try this...
- Close Godot
- Open the
project.godot file in a text editor
- Find the
[autoload] section in the file
- Find and remove the offending entry
- Save the modified file
- Restart Godot and see if the contents of the Autoload panel look correct