The Aten from the Flamel books is modeled after the real Aten of Egyptian mythology.
So, technically, they're the same Aten...
And the Aten from the past is also the same Aten of the present. We may be seeing two Atens from the books but there's just one Aten, really.
Unless the Aten from the present travels back in time in Danu Talis to meet his past self, then we'll see two Aten talking with each other.
Time travel is really chaotic. I'm like
when reading about time travel.