Not if the libraries used across the OS (new and old) are updated and kept the same. That then means apps can pretty much be brought back and forth across OS. Of course certain device specific features won't work (e.g. say if an app uses multi-touch).

If Nokia doesn't want to officially support MeeGo, fine. With the way they've been cutting features out of Maemo that I'm use to having I'm not so sure I would want whatever's next (there were talks about a DRM locked system). But they should be more active in the development of Mer as a replacement to the previous Maemo operating systems then.