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Yes - you can have a second library in Calibre, although in most cases it is easier to have only one physical library and create 'virtual libraries' by using tags.
If you have more than one library then every time you want to switch libraries you will need to go into the Calibre Preferences to switch to the alternative library. You can also specify the library to be used when launching Calibre by using "--with-library path_to_library_folder" as a parameter to the launch command.
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