Yes, the library is completely separate. But I don't know if uninstalling calibre also removes the configuration directory, I would verify that it's gone. Open the configuration directory before uninstalling (see directions in a previous post for how to open it from within calibre) and after the uninstall is complete verify the directory is gone. Then you can reinstall calibre and choose your old calibre library directory and it'll Just Work. You'll need to reinstall all the plugins and make any settings changes again, but the library will stay as it was.
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