In retrospect John seemed to feel confidently resolved about Edward’s atheism. He seems to be free of any conflict, certainly free of any animosity, about Edward's embrace of atheism. Two of the things that point to this are the fact that John keeps Edward's old baseball mitt on his desk and that he writes that he feels he has "been talking to him" his whole life.
[T]hat old glove of Edward's that I keep on my desk. No webbing at all, no pocket to speak of...
The clearest demonstration we have in the text that John seems to feel confidently resolved about Edward's spiritual condition (his atheism) is the happy time they shared playing a heated game of catch.
Edward has returned to Gilead, now the learned "Herr Doktor" and sporting an impressive mustache, having gotten his advanced degrees in ancient languages in Göttingen, Germany, a university town in Saxony. Rejected by his father's wrath over his refusal to participate in the family custom of asking a blessing before dinning, Edward and John eat a quiet meal, then walk together to Edward's hotel.
On one other day, John sought Edward out at the hotel. On a "dusty little street and a hot day" they got into vigorously throwing grounders and flies to each other. People stopped to watch the sight. Edward, with his coat off, "his collar open and his suspenders hanging down at his sides," had poured a glass of water over his head, the water running off and dripping down his mustache.
In this aspect, with water dripping, he quoted to John a portion of Psalm 133, which references brethren together in unity and precious [anointing] oil running down their beards. John lit up with recognition. He understood that Edward "knew everything [he himself] knew, every single word."
John saw Edward's knowledge two ways. As a Calvinist, he felt that since Edward knew everything, his soul was secure. He also felt that although he knew everything, his mind was not persuaded by it (the mind may not be logically persuaded but his soul may be secure through predestination). John's feelings in retrospect are the same as they were on that day: all was and would be good.
Behold, how good and how pleasant it is,
For brethren to dwell together in unity!
It is like the precious oil upon the head,
That ran down upon the beard; ...
Like the dew of Hermon,...
I have often thought what a splendid thing that was for him to do. I wished my father had been there, because I knew it would have made him laugh.