> Either atoms exist or they dont

Perfect example, since they only exist as a concept to describe an observation. With higher precision of observation, it became “the new truth“ that most of the time even on the observation level do not actually exist in terms of matter; they “flicker“ fast enough to appear existing at all times. When you look often enough or at the wrong times, there is nothing to observe.

> When you look often enough or at the wrong times, there is nothing to observe.

Is this because atoms don't exist, or because we are looking in the wrong way due to partial (mis)understanding?

The "new truth" that you talk about is just a different understanding of the concept of atom, but the actual thing that we call atom and that exists in the real world (whether as matter or in some other form) has not changed.

Exactly the right question. If atoms are forever retained as a locally true-in-its-domain and at-its-level-of-description phenomena in every future theory, I think they count as real in any important sense. Even classical mechanics is true in the sense of strongly accurate and predictive at its scales of description, as an approximation of something more precisely described by QM.

One thing that gets me excited is that there's a tantalizing possibility that the 21st century might have an Einstein-level breakthrough that treats holography and some principle of informational consistency as more fundamental than QM, which is amazing, and would change everything.

But even in that hypothetical future paradigm, an "atom" would still be something true and meaningful against that backdrop, and our measurements or knowledge claims about it would still be meaningful. And our progress toward knowledge of the atom was still real progress.

It's legitimate to treat our knowledge as limited, subject to revision, or approximating. But treating that grain of truth like it implies no knowledge or progress is in hand is an abuse of the concept.