Problem Solved
Finally, this problem is solved. Thanks for all the suggestions. Here's what you have to do. For each book that has the multiple, repeated bookmarks:
1. In the eBook Library, delete the book from the collection and the "Books" section. This will not remove the corresponding file from your PC so you can re-import it later.
2. Plug in your eBook Reader and go to the book. Using the "Info" feature, write down the filename so you can re-import it later.
3. In the eBook Library, go to the "Reader" section and delete the book from the collection and the "Books" section.
4. In the eBook Library, do a File | Import Files... and find the filename that came from the eBook Reader. Move it back into your collection. Drop the collection to eBook Reader.
Lots of steps - there might be a more straightforward way. But I followed this process for each book with the offensive bookmarks and now the eBook Reader is perfect. It's a little thing, but with so many copies of bookmarks from books I finished, it made the feature unusable and unappealing.
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