Aye, as I said, that was Chakotay speculating. The only tangible proof was the Voth's dna, which matched ours. We have no way to know if what Chakotay said actually happened.
I insist on this point because it means that criticizing this episode on the basis that the Voth left no traces back on Earth isn't fair.
I for one consider this to be one the best Star Trek episodes, a classic allegorical tale.
Well, aside from some "Peacekeeper" revelation (Farscape), his deduction is most logical. But you're right, it's all just speculation.
As far as the "left nothing on Earth" complaint, other than bone, do we see anything else older than 65 million years old? For all we know, they lived under water.