Hola Alan

We've just taken that specific question out of that lesson because, as you said, cases with 1000 are not mentioned in the lesson. This lesson is only dealing with the units, tens and hundreds. I've noted it down for a more advanced lesson though. 

To answer your question about 2001 years, we would say "Los dos mil un años...". As you can see, "mil" doesn't follow the same rule as the hundreds, e.g "los doscientos un años...".

Note that the example of "Las mil y una noches" is a bit special. We keep the "y" here because that is what used to happen in the past in Spanish language, and the title of this very famous book is always said this way.

I hope this note helps until we have the new lesson ready.

Gracias por tu contribución.

Un saludo

Inma