To make up.

Since they had a little bickering in Rewinding town, Lenalee hadn’t talked much to Allen. It was clear that Lenalee hadn’t forgiven him yet.

After the fight was over, both of them fainted because of the wounds they had before Miranda started the invocation. When Allen woke up, he was in a hospital, and Komui was with him. He said that the town returned to normal, and that they would be assigned to a long mission afterwards. Here, Allen got to know an old man who adressed himself as Bookman, and a red-headed boy named Lavi. They were bookmen as well as exorcists.

Later, Allen came to visit Lenalee, but she hadn't woken up yet. Lavi then had a talk with Allen outside, and then they realized that the town was surrounded by akumas mixing in with humans. These akumas also attacked Komui's place. Fortunately, Lenalee woke up and saved his brother.
When the situation got better, Komui told them about The Earl, who had started to make a move. He had been stealing Innocence and searching for the Heart. He killed a general of the Black Order in this mission, because generals might have bigger chance of being the possessor of the Heart. Thus, Allen's mission this time, together with Lenalee, Bookman, and Lavi, was to guard one of the four Generals—and that would be General Cross Marian.

The team then prepared to set on the journey to find Cross. They got on the train. Allen went to the restroom to wash his face, and then he found Lenalee outside. He asked out of curiosity: "Lenalee, what are you doing here?" Upon hearing this, Lenalee just smiled and said "Nothing", but obviously she was angry. She stepped away quickly afterwards. She was probably there because she was worried about Allen (his left eye still hadn't healed so he couldn't detect akumas), and Allen's plain reaction probably didn't make her feel any better. Even when they rejoined with Bookman and Lavi, Lenalee avoided eye contacts with Allen.

When the train stopped and Lenalee went out to buy some stuffs for lunch, Allen managed to get some time alone with Lenalee and apologized to her.

Allen: "That... Come to think of it, we haven't really talked since that time... About that time—" (bows down) "—I'm really sorry."
Lenalee: (puts the paperbag over his head) "Don't lift up your head!"
Allen: "Huh? Ah... Alright."
Lenalee: "Because I still haven't forgiven you yet. You're so selfish, Allen-kun. 'No one can see Akuma's soul but me'? Carrying all the burden by yourself... Sacrificing yourself in the battle... Just what are we friends for? Why can't we fight together??" (cries and falls to her knees) "I hate it. Allen-kun's left eye... I hate it..."
Allen: "Sorry... Lenalee... Thank you for helping me..."
Lenalee: (glares) "Get used to it, because I'll always help you!" (snatches the lunch and gets on to the train)
Allen: (thinks) Does that mean she forgives me...?

As seen from the dialogue above, Lenalee hated Allen for his self-sacrifice. What she mentioned was quite correct, because Allen probably relied, or had people rely on his left eye too much. And his saving Akuma's soul is on the top priority for him more than anything else—so much that it turned his head away from other things; even his safety and the existence of people who cared for him. I see that from this quarrel with Lenalee (which is sort of cute, I think), Allen changed a little. On later chapters he was still as self-sacrificing as ever, but he had his friends (or World as Lenalee refers) kept in mind. They weren’t seen to be involved in huge arguments anymore ever since.