Given how many works survived simply due to dumb luck rather than deliberate preservation, I'm not convinced what we have is the "greatest hits" list. Consider how much of early silent film has been lost. Sure, based on contemporary accounts we have many of the most popular works, but the completeness drops off very sharply. Consider the filmography of Mary Pickford, an early superstar, whose filmography is considered "largely complete":

https://en.m.wikipedia.org/wiki/Mary_Pickford_filmography

Take a look at how many of the films have "lost" in the rightmost column. Several dozen films from the middle of her career are completely lost, and that's despite efforts that Pickford herself made to track many of them down.

Now, film had special factors that accelerated these losses from spontaneous combustion when stored improperly, to recycling for the silver content, changing technology and fashion, to being considered ephemeral in the first place. But some of these amenities have0 by their parallels for the written word, and a much longer period of time for the works to be lost.

In some sense that's tautological. We know some publications exist that others thought were great works, but those have been lost, so we cannot now say they are great works. https://en.wikipedia.org/wiki/Lost_literary_work

> for some reason

Had the fire at Ashburnham House burned the sole copy of the Nowell Codex, we would not now have Beowulf.

Had Max Brod followed Kafka wishes, we would not now have The Trial.

So the "reason" can be happenstance, and not due to how we currently regard its place in literature.

The question then is, what other works might we now regard as "great", but for happenstance. Some may even still be available, and simply unread for centuries, waiting to be rediscovered.