I think you're misunderstanding the meaning of them saying the flashbacks are no longer pertinent. Some things have changed for the characters on the plane - Hurley's lucky instead of unlucky, Kate may actually be innocent (as she hinted to Claire), Sharon did not return with Boone from Australia. Even minor things changed in that timeline, like Jack being handed one bottle on the plane instead of two. Other things have not changed (though the things leading to them may have) such as John's paralysis or Charlie's drug addiction.
The flashbacks are still the true history of the characters on the island, however - and isn't that the version of events that we still find more compelling, the one that we feel is their true story? I have to believe that the "alternate timeline" will serve to frame the end of the true (island) characters story, to give it context and meaning. The versions of the characters that we know and love continue to have their original backstories.
- D