True, but what about LF finding the valley? I seem to remember them referring to it as they did it in the cut version.
I think he means the original ending that's intact on the soundtrack and in the novels, where Littlefoot finds the Great Valley shortly after Cera splits the group, only to return and save the others. This, certainly, can't be considered canon any more, since it would contradict the ending as it was released. Everything else that got cut can easily fit into the film though...Sharptooth's damaged eye, Cera's racism towards Spike when he hatches, the meeting with the "Crown-Heads"...just cause we didn't see it on screen doesn't mean it didn't happen.
The only way the original ending would ever become canon would be if someone made a "Director's Cut" special edition of the film that included a properly animated version of the scene. Course, as has been said many times before, the scenes don't exist anymore, so somebody would have to animate them from scratch!
To go back to your original question though, I don't think the sequels have been affected much by the cuts to the film...any character development that would have been obtained during those scenes still got resolved in some way anyway. For instance, Cera's big scene where she would have ditched her racist attitudes once and for all (in the scene with the Crown-Heads) got cut, yet she still loses this over the course of the film, and this carries over into the sequels. If anything, the sequels have been affected by the sequels...Cera's mother and siblings not appearing in the second film, and then becoming non-existent after the third film?
The new staff that was working on the sequels might not have known about these scenes. In short, the cut version is canon. It's like that Disney movie where the protagonist mentioned fighting a giant squid, but the scene was deleted. This is, however, the opposite.
That would be "The Goonies", I believe! Great film!