Creating a new plugin is best done through the ProjectSettings under Plugins > Create (top right)
Messing up the editor nodes happens quite a lot. When it does, you can use the Reload Current Project button
from the top menu > Project. If it happens often, you can also set a shortcut for it.
Useful in combination with that is the EditorSetting (not project) to re-open all scenes which were previously open.
You can find it under this path interface/scene_tabs/restore_scenes_on_load