This is from a letter she wrote in reply to a friend's letter.
"I think the experience of losing your faith, or of having lost it, is an experience that in the long run belongs to faith; or at least it can belong to faith if faith is still valuable to you, and it must be or you would not have written me about this.
I don’t know how the kind of faith required of a Christian living in the 20th century can be at all if it is not grounded on this experience that you are having right now of unbelief. “Lord, I believe; help my unbelief” is the most natural and most human and most agonizing prayer in the gospels, and I think it is the foundation prayer of faith."
Read the rest of the letter here:
http://www.bruderhof.com/articles/o-connor-faith.htm?source=DailyDig(The Bruderhof are a Mennonite sect that live communally and are pacifists. They'll send you a daily quote if you sign up and their site has many articles, poems, and e-books. They have collections of readings for Advent and Lent, too.)
BTW, I haven't checked the Gospels, but I think Flannery misspoke. I have always seen the prayer "Lord, I believe; help my unbelief" associated with St. Augustine.