What does the cover Look Like?
Is it a Calibre Generated one (it will have words on it)?
IIRC a missing cover will just show as a Blank version of the Calibre one in the details pane as it does not really have that file.
The other possibility is someone has been doing stuff beneath the skirts, therefor Calibre is not aware of ANY kind of change.
Run the full Library Maintenance and resolve those issues found.
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