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.