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Updating Calibre is always a reinstall of the entire Calibre application, so that will mean it adds a shortcut back to your desktop if you had removed it. So don't worry about any of that - updating should preserve your configuration files with all your Calibre settings.
Updating also won't delete your library, though it will update it sometimes as required for the latest Calibre version. I am no expert on recovering from failed upgrades but I am sure one of the regulars will come along to assist. It may help if you post the answers to these questions:
How old was the version you were updating from?
Did you backup your library before you updated?
Do you see any output when you start calibre with calibre-debug -g?
If you look at the folder where all your books are stored, does it still exist? Is there a metadata.db file there?
If you can still see your folders of books in the Calibre filesystem (upgrading Calibre will never touch those) then worst case it should be possible to rebuild your database. However before you go down that route there may be a simpler explanation - like for instance do you need to switch libraries?
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