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By any chance did you rename the koreader zip file? It expects the full filename, afaik. If it hasn't been renamed, you should probably report the bug in the KOReader thread or on github.
Last time I updated (maybe around July?), an overwrite/merge with the package contents was fine.
Last read position, bookmarks and highlights are stored in a .sdr folder where the book is located and not in koreader. The settings and cache are generated upon initial use so they're not present in the zip file (hence, nothing to overwrite with).
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