I'm guessing that they will, at least, make the "bookshelves" mutually accessible. That guess is based on three things:
1) eReader already has access to the Fictionwise bookshelf, at least I know the Blackberry version does. I can download any of my multi-format FW purchases OTA to my phone.
2) B&N already claims interoperability with eReader (for lending and synching).
3) It would just be silly not to, especially if they want to convert existing FW customers to their own device.