I doubt they'll stop selling ePub 2 books, any more than they stopped selling ePub 1 books. New books may be made to the new format--but should still be readable on older devices/software, to the limits of the current format. Which is to say, footnotes may disappear or be visible as endnotes.
It's possible the newer ebooks won't be readable on older devices, but I'd expect that transition to take quite some time. Hardware sellers are aware that "you must buy a new device to read next month's books" is a good way to lose long-time customers to the competition. Plenty of people will decide that, if they have to buy a new device anyway, maybe it's time to try a Kindle or Nook.
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