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The bookmarks should be stored on your card, so even if the reader ran out of power it shouldn't be an issue.
The firmware upgrade could possibly have affected them, but it's unlikely... did you just do it before you noticed they were gone?
A more likely possibility is that you perhaps moved or renamed your books/files? The bookmarks are stored separately, and in that case are longer linked/in sync with the original book they were supposed to go with...
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