Not every game will be able to make the leap. Those games probably just won't be sold at all.
To be fair, though, not having "Phantom Hourglass" on the service is actually a pretty big plus.
I actually enjoyed Phantom Hourglass. As a handheld Zelda game, I thought it was very enjoyable. I didn't expect it to be on-par with the home console releases, so I wasn't disappointed. But Spirit Tracks was one pull too many on the same taffy.