Harry doesn't react like other boys do to the allure. Because of his mother's protection when he comes in contact with Veela allure Harry feels love and comfort and warmth, like being held in his mother's arms.
During the TWT Harry feels that warm feeling again and wanting to feel happy instinctively grabs it and wraps it around himself. Fleur feels her allure being actively tugged and pulled on when she's in the main hall of Hogwarts. Curious and a little afraid she begins to try to find what's happening and writes to her mother about the sensation.
Within the next weeks Appoline does what research she can and eventually decides to accompany her family to Hogwarts during the second task to help Fleur look into the event.
Cue Harry being himself and saving an adorable little girl. During the fallout of the second task Harry finally relieved of dealing with people allows himself to relax and feels the happy warm feeling and wraps it around himself, Fleur and Appoline feel it and are able to figure out that it's Harry.