A plugin file IS empty. A plugin file contains nothing, the master file contains everything. These are two seperate objects, do not think because you loaded the master that your plugin file will contain all of that because it will not.
When you start making changes, or adding stuff that is different or not in the master, then it goes in your plugin file. Now your plugin file is not empty.
If you start deleting objects from the master, your plugin file will remove them from your 'entire game'.
So you NEVER delete master file objects. You can replace 'objects in the render window' with other objects, or move them out of sight, but you never delete them. This can cause your game to crash to desktop, or at minimal, put holes in vanilla cells.
Your plugin file MODIFIES the master file before the game starts. So if you start deleting stuff, it will be gone from your game entirely.