I am sincerely interested in this issue. You and I once met, Derek, at an aesthetics conference (perhaps it was in Uppsala or at the Scruton's Aesthetics Conference in Durham). We share an interest in Malraux. I believe him to be one of the few who understand the connection between an artwork's place in the history of art and an artwork's value. He understands the importance of style, a hopelessly under-discussed topic in analytic aesthetics.  

Anyway, one response to your concern, and a cheeky one, is that the definition of 'great artwork' implies that any work we bestow with the honorific 'great' is one that has endured. There will be no great artworks that have not endured. If this is so, then bestowal of the honorific may be less about a capacity to transcend time than a result of our intuitions about the application of a concept. That would be sad, but it might be true.  

If we conceive of enduring artworks as ones that are great in virtue partly of having endured, which we might do, then there will be no artworks that have endured which are not great. I am less inclined to accept this direction of implication. A work might endure because of the effect of its shock value, and I doubt that the capacity to shock is sufficient for something's being a great work of art. Duchamp's fountain might be like this. An artist's canned shit -- I don't know if anyone has done that -- would surely be like this, if it lived on, say, with the help of mention in art theory books, etc.  

That sort of thing aside, though, my best response at this point is to say that some artworks endure and are great because of a single complex feature that gives rise to both greatness and endurance. It gives rise to a greatness that they possess regardless of our preferences and an endurance that is a function of both that greatness and our response to it. This is the feature of being an exemplar of an artist's style that is partly original -- different from previous styles -- and partly similar to previous styles. They take a place in the art historical chain of ever-evolving style.

If one buys that story -- and I can think of few other stories that can make as much sense of the artistic problems that artists set for themselves -- then one is led immediately to a follow-on question: what is the connection between such a style and the very great value we take great artworks to have? That, anyway, is my take on the matter. But as far as I can see, it is also Malraux's.