The folder is also the Library name.
Somewhere along the line, you relinked to a lost Library (path change?).
Note: If Calibre can't find the 'last used' Library, and it can't find the default name, it will create it
Having 2 with the same name is not fun.
Switch to the 1 book: then right click the Library icon: Remove Library: Calibre Library
Only non-active show up
This only deletes the Link. It does not touch the folders.
Now Using the O/S explorer. Find the real Library (search for Metadata.db. the one with author folders is what you want). Rename that Parent Calibre Library -> <something else. eg Main>.
Back in Calibre, now relink
Right click the library icon: Create/Switch:Use existing:<point it to the new named folder>