If think what may have happend is...iF when you bought the book from each site you used the 'sync' button at the bottom of the kobo app it would sync your kobo with the online libary. In you case the borders book was not in the kobo app libary so it was erased adn replaced by the kobo apps libary.
What I do is buy from kobo books (the website not through the kobo applicaton) after you confirm your purchase there is a button that says something like 'download adobe epub' chose that and then Adobe digital editions starts up and downloads the book to a folder on your computer (on mine it goes to [documents]/[my digital editions].
If your kobo is pluged in and on manage you can drag and drop from ADE to your kobo or if you have calibre installed you hit 'add books' navigate to the my digital editons folder and then add the book. once the book is in calibre you hit the send to device button at the top of the calibre window and boom your book is there. When you add books via calibre or ADE they dont replace the ones that are there like syncing through the desk top app does.
Calibre is essentially itunes for your ebooks. FWIW I exclusivly use calibre to manage my library and just use ade to downlod the epubs.