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How did you delete the PDFs? If you deleted using Calibre the links should have cleared automatically.
If you bypassed Calibre and deleted the PDFs directly from the file system then you have corrupted the database.
To repair a corrupt dtatabase:
1. Under Library, select Library Maintenance and then Check Library.
2. If there are no other errors you will get a "Success" message. Click Yes to check if the files in your library match the database.
3. You should see "missing books formats (fixable)". Click the check box in front of "fixable" and then click Fix Marked.
That should do it.
Edit - I see several of us were typing at the same time.
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