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You have probably confused Calibre because the library folder it was using no longer exists?
The easiest way to fix it will be to click on the Library icon and use use the option to switch libraries and point at where the library now is. You can use that option to switch to an existing library folder, or to create a new library folder. Note, however, that this will lose any of the books that you say have been dumped into your home folder so they will need re-adding.
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