Faith in Atheism

Imagine if God existed but was sufficiently advanced such that we couldn't identify him for another 1000 years. Where does that leave the scientific atheist? I know that CS Lewis has already gone through this exercise, but it would be interesting to discuss. That is what is the basis of the premise of atheist evangelism?

Christopher Hitchens went through this with Al Sharpton and others early this year or late last year, I can't remember which. Hitchens found a great deal to admire in Sharpton's apologetics. I wonder if most atheists measure up.

Question.
Does the atheist take the non-existence of God on faith?

Question.
Where does the non-existence of God place the locus of moral discernment? IE what human mental process is short-circuited when a faith-based morality is argued?

Question.
Do you see the problem here?