Thanks for your interest. I have sorted myself out.
First, I used the Library Maintenance tool to make sure everything was in good shape.
Then I discovered uned Bulk edit metadata the option to set the cover from within the ebook which restored most of the covers (why this option is not available for editing the metadata individually I'm not sure).
Can't think how I lost the covers. I moved the location of the Library, and of over 5000 books, only about 50 retained the cover.jpg file.
Ah well, mostly sorted now.
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