Just a update for anyone who encounters similar. All of my files were there just somehow renamed cover - Copy.jpg filename - Copy.epub etc. Seems that a copy utility can do this sometimes.
I backed everything up and used a renaming utility after careful testing on a small subset and my database check and files check are 100% good now.
I will find the solution you suggested useful, as it does seem to happen with one or ten books on a regular basis, but several thousand covers to extract and epubs etc. to rename was just too tedious to contemplate.
Thanks again
Helen
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