Here's how I took it to happen. As a boy, all Davros knew was that he encountered some guy. We're still not sure what the Doctor did.
At any rate, the Doctor had Capaldi's face and if there was no name associated with it, Davros wouldn't link this stranger to the Doctor. At least not until the Doctor regenerated into Capaldi. At that point, one of Davros' associates may have identified him. This allowed Davros to rememberthe incident, or at least correctly associate it with the proper identity.
Maybe it's something else entirely, but that's how I interpreted it given what we've seen so far.
Mr Awe