Yeah, it doesn't work that way. When you copied the one library over the other, you probably wrote over the metadata.db file in the root of the library folder, which is the database folder Calibre uses for its library.
If you want to merge libraries, use the copy to library- feature you get when using multiple libraries: Switch to the second library using the library dropdown menu, select the books you want to copy and right-click. You should have the option to copy in the menu.
Since you've already seem to have overwritten your metadata.db, you basically have books in your library folder that Calibre knows nothing about. Your best bet would probably be to create a new library at another location and importing the books from the old library using the "subfolders, one book in different formats" option in the add books dropdown menu.
The thing to remember when using Calibre is that manual operations inside its library folders are almost always a Bad Thing. Reading can be okay, although metadata consistency with the database is not guaranteed, writing is always a bad idea. The best way to use Calibre is to view the library folder as a black box and use the GUI or the command line tools to interface with your library.
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