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The Borders Desktop app downloads everything into this ever-growing sqlite database which is very tricky to extract things from.
For best results in liberating your Borders books to read on the Kindle (it can be done!) is to go back to the website, check your My eBooks Library listing, and do "Download ePub" for the book you want.
Open the .acsm file you get in Adobe Digital Editions (it's like a pointer file to the real ePub, which will then download), and then once you've gotten it, use the ePub file in the Digital Editions downloads folder for further tweaking via whichever set of tools you're using.
Hope this helps.
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