How to save Scene Hierarchy if delete Lib dir?

At first I create a unity3d project, which scene hierarchy:

because Lib dir which in unity project is too big, so I delete this dir.
then I open the project, unity3d create a new Lib dir, scene hierarchy changed:

How to save Scene Hierarchy if delete Lib dir?

The Library directory is exactly as big as the project needs it. Deleting it to free up space is like deleting Unity itself because it’s too big, but still expecting to work with it. It doesn’t make much sense.

Aside from that, the Library folder of a Unity project contains nothing that cannot be reproduced from the Assets folder. It contains the imported assets. For example, if you put a 3D model in your Assets folder, Unity won’t open and display your .blend or .3ds file. It will instead have the file converted to an fbx model and load and display that instead. This fbx file is stored in the library. When you delete your Library folder, Unity will determine all the missing imported assets (which is: all of them) and reimport them. This makes it so unnecessary to delete the Library folder unless it is corrupted - all its contents are going to be reproduced anyway.

Now for the scene hierarchy. Your scene has not changed because it is in your Assets folder. If you delete your Library folder, you might have deleted an internal representation of the scene file, but not the scene file itself. You just have to open it again by double clicking the scene file in your Project View.

If you didn’t save your scene into your Assets folder in the first place, deleting the Library folder is not what caused the problem.