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It sounds as if something is interfering with Calibre's library access. The fact you mention retries seem to work suggests it is not a problem with fixed permissions as it is dynamic in some way.
It is worth making sure that the Calibre library folder (and sub-folders) are set to be excluded in your Virus checker. Ebook files are not candidates for viruses, and also it can improve performance. Virus checkers are one component that tends to be updated automatically at regular intervals and that can interfere with the operation of other programs.
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