[JohnnyBook]

I believe.... Calibre is not changing the author or title folder when you change the metadata.

Its creating a new folder and moving the files to the new folder.

The files it did not recognize (and therefore did not move) are still in the original folder where they started.

John Smith (folder)
First book (folder)
First book - John Smith.mobi
cover.jpg
Alt Cover.jpg
Alt2 Cover.jpg

Renamed to Johnny Smith

The book and cover will be moved to the new folders (Johnny Smith/First book)
But the Alt covers will still be in (John Smith/First book) EDIT: Nope the folder and Alt covers are deleted

Because Calibre does not see them in the original folder cause they are not in its database.

EDIT: Correction: looks like the original folder and the extra covers are being deleted after the book files in the database are moved to the new folder.

So if you want to keep the Alt covers until you decide on which to choose, you can NOT rename the author or title of the book.