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I am only guessing, but I am thinking that your ebook library software is also keeping a copy of those bookmarks for you.
Depending on how cleverly they are hidden in the software, it might be easier to uninstall the software (make sure that the program folders are deleted also in the various locations on your hard drive) and the nreinstall the software.
Most ebook retailers also save your purchase information incase you have to redownload your books, so puttintg all your purchases back in the software should not be a problem, but make sure you can retrieve your books before deleting the software, or make a manual backup of only the ebooks before the deletion.
I hope I have explained this clearly.
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