Yes. Move the metadata.db and create a symlink where it originally was, to the new location. Repeat for each Calibre Library.
I believe you have to specify both path and filename in both link and target. But I haven't tested it.
mklink "X:\Books\Calibre Library 1\Metadata.db" "C:\Calibre Portable\Metadata\Calibre Library 1\Metadata.db"