[Horus68]

If you don't want it just delete the folder you do not need anymore (in windows).
Then, if you go to Calibre and switch library to the one corresponding to the folder already deleted, calibre will ask you to remove that entry from the menu.

EDITED: The rename library on my previous reply is not required just an easy way to make sure you are able to see what folder is what library (as both have same name)