This has happened to me when I moved the library to another location. The covers were still there (in the books themselves and most were in file folders) but didn't show up in the gui. Not knowing what do do and having probably not much else to do that day, I just dragged the covers to the Gui. Maybe I could have just recopied a recent backup metadata.db file and done a library check, but this was an afterthought.
Helen
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