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You can run both apps on your computer but when you sync your kobo, whatever's in the app you use will replace what's on the kobo. By native, I mean the one that's tied to kobobooks.com, not borders.com.
If you can get EPUBs for all your Borders purchases, you could certainly switch over to the native app permanently. That's what I did as I had lots of pre-existing purchases with kobobooks.com and none with Borders, outside of the eReader itself.
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