Ages of the Valinor and the Ice Ages.

[Legate of Amon Lanc]

Originally Posted by James the Just

Not long after, though, there came the Toba catastrophe, a supervolcanic eruption, wiping out most of mankind.

https://en.wikipedia.org/wiki/Toba_catastrophe_theory

What happened then? Who knows?

It would make sense if it was a first attempt of Morgoth to destroy the Atani. Perhaps it seemed to him at that point that destroying them could be the safest course of action if he for example realised that he could not turn all of them to his side. He would then further revise his plans later.

Originally Posted by James the Just

I imagine that Elven bones just kind of fade away over time, explaining the lack of physical evidence.

Well I would also imagine most of the Elves did not die. Those who would would die violently. But they are immortal otherwise, after all, so no reason for large amount of bones.