I was about to write this as a comment but then I noticed it got a little lengthy so I wrote it here.
Anyway, I read this chapter and didn't understand what happened at the end. And then decided to read it two more times, and finally was able to grasp a few things.
The real problem comes from what she said in the ending which clearly illustrated that not she had no idea what he was implying, nor did she even recognize who said it to her. Like an erasure of memories.
But then I reread it.
Looking from the beginning and then the end, you can note the time on the clock and the place that they meet is exactly the same. But it doesn't really feel like a whole day passed. Rather, there's no real sense made if a day passed. They simply reverted back to the beginning.
At this point I see two possible things.
1) Whatever was making her feel down in the beginning was actually a result of one of those bugs that he mentioned.
2) He used the monolith to change something. Inserting it back at an angle could have caused changes on its own.
In this case, the bug or the change might have been that girl that he mentioned she liked. "She wasn't right for her". Blowing on it might have prevented the bug from persisting and changed history right. Inserting it in improperly might have changed something, almost like a hack. But it's fine since something like this will be forgiven. If his direct motive was to change how she felt about that girl she once liked, the hidden purpose behind that line might have been a hint towards God's disapproval for homosexuality. Of course, there is also something in it for him, since he obviously likes her. Whether it happened because of force hacked history or the result of a removed bug is impossible to tell, however, this is really just me going on about what I gathered after reading that part of the chapter three times.
Perhaps I'm just thinking too hard. Whatever, I wrote too many words to not press send.