Migrating and folders issues


My project is working just fine, but I have some issues with folders, migrating and other stuff. I was cleaning it up and I was trying to remove starter content, but somehow I couldn’t delete it. So, I did it through windows explorer and it worked, but:

First of all, I have different folders in windows explorer and different in editor.
Secondly, some empty folders disappear and some folders with assets come back to life after deleting them.
Thirdly, I can’t migrate a map to my project from a different one. I tried migrating and copy/paste through explorer - the map opens, the assets are there, but any object from the scene loses its reference to an object (static mesh).

Anything I can do about it? I tried fixing up redirectories, but it helped only at the beginning…