I always assumed that Thanos just did what he said, "reduced them to atoms", and that they more or less still "exist" in a non-tangible form with no current method of reconcentrating/recombining them.
Going off of what the Collector said:
"Before creation itself, there were six singularities. Then the universe exploded into existence, and the remnants of these systems were forged into concentrated ingots... Infinity Stones."
What the Eternals intro text said:
"In the beginning... before the six Singularities and the dawn of creation, came the CELESTIALS. Arishem, the Prime Celestial, created the first sun and brought light into the universe. Life began, and thrived. All was in balance."
What Wong said:
"At the dawn of the universe, there was nothing. Then... Boom. The Big Bang sent six elemental crystals hurtling across the virgin universe. These Infinity Stones each control an essential aspect of existence."
And this page from the GotG Art book:
It's either the "Big Bang concentrated the Six Singularities, created by the Cosmic Entities, into the Six Infinity Stones, and sent them out across the new universe" or the "Cosmic Entities concentrated the Six Singularities and the Big Bang sent them across into the new universe"