[Quoth]

Pretend the Library folder doesn't exist. It's part of Calibre's Database because ebooks as files works far better than importing into an actual SQL database (I tried that once with documents and a seriously expensive SQL Server and while in theory possible it's stupid. It might not really "work" on SQLight which doesn't work the same way as MySQL, Oracle, DB2, MS-SQL or MariaDB).

There are ways to copy the Library files, but you need to have Calibre closed and copy the *.db files too. It's better to use Export and Import to copy an entire library, or Save to Disk, then Add Books inside the two Calibre libraries if just a few ebooks.