I made a square hole in the plane with the modeling tool in one of the projects, but after creating a new project the hole is still on the plane, How do I restore the plane to its original form?
Sounds to me like you edited one of the engine assets from one of your projects. In that case you could do a clean reinstall of the engine.
To restore your engine assets, have you tried verifying the engine through the Launcher? You should just need to click on the arrow next to your engine version and click [Verify]. The process may take a few minutes.