The art of mind-reading, she performed it well. I am impressed by how Lenalee could tell what Allen was thinking.

The first time she showed this ‘ability’ was when Allen apologized to her after their fight in the Rewinding town. In the train, Bookman said that they needed Allen’s eye to heal soon because he could detect akumas. Lenalee had a sad look on her face in this scene. She seemed to be thoughtful, somehow. And this is what she said when Allen apologized to her:

Lenalee: 'No one can see Akuma's soul but me'? Carrying all the burden by yourself... Sacrificing yourself in the battle...

Oh, wow. So that was what was behind her wistful look. Lenalee had already learned about Allen: his special akuma-detecting eye made him has a special ability, as well as an extra burden to himself. Allen felt that the others relied on him because of that eye—and that was what she thought, and it shouldn’t be left that way because they were partners, working together.

The next time she read his mind was after Allen and Lenalee reunited in Edo. When Lenalee was resting, Allen knelt down to see her, and the first thing he said was an apology—recurring apology.

What do you think did this apologize refer to? Other people might get the wrong idea. Maybe Allen was just saying sorry because he came late, or that his absence made Lenalee go through some pain. But no, Lenalee already knew. She sat and reached out a hand to touch Allen’s cheek.

Lenalee: “What are you sorry for? If it’s about Suman, you already saved him... I’m sure Suman’s heart feels saved by you too, Allen-kun...”

Allen still remembered Lenalee’s desperate request to save Suman, and that he failed to grant her wish. Lenalee, too, couldn’t forget how her wish had almost taken Allen’s life. Only Lenalee knew how painful it was for him to have failed rescuing a comrade. She also knew how to make him feel better. Her soothing words made Allen shed a tear. And the most notable moment in this scene, to me, was when Lenalee smiled and welcomed Allen.

Lenalee: “Welcome back, Allen-kun.”
Allen: “...Back... I’m back, Lenalee.”

Remember Lenalee’s first welcome message to Allen? I’m sure Allen was reminded of that sweet moment as well. It was a precious moment, where Lenalee knew what she believed really turned into realization, Allen had the burdens unloaded, and felt accepted once again—finally—after what he had gone through.

It was also shown in chapter 120, when Allen, Lenalee, and Cross were ready to leave Noah's Ark. Allen seemed thoughtful. Lenalee noticed this, and then talked to him.

Lenalee: “Allen-kun? Even if there is a door, do you think that you can’t go through it yet?”

Allen looked surprised upon hearing that. Maybe he didn’t expect that Lenalee could tell what he was thinking. But then, he smiled, and said without hesitation: “Certainly.”

Lenalee could tell what Allen was thinking. He wanted to let the others go ahead while Allen himself would go back to find Kanda and Krory—because they were also their comrades in the Black Order—their family. They both were important for him, and for the others. She didn’t like the idea, but she knew he would do that if she were in his shoes. They knew that it was for the best. This idea, however, was never realized, there was a much better alternative they never knew before.