If the full-size covers got transferred durring a Save to Disk then they probably got copied to the same directory as their matching book.
In Internal Memory, books are normally stored somewhere beneath the [Drive:]/database/media/books/ directory. Exactly where will depend on the Save Template you used for Save to Disk.
On an SD card, I can't remember exactly which directory is used because I don't store books on an SD card. It won't be difficult to find out if this is where your problem lies.
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