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Hi wrenn1,
We're working this as well. For now, it may be easier for you to remove the books from your library using the website as you described. Note that you will always have access to the books you have already purchased (even if you remove from your library).
Once you remove, you should wait for about 30 minutes to be safe and update your desktop application library again, and those books should be gone.
Hope that helps for now.
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