Yes, Rowdy and Junior's friendship is indeed restored by the conclusion of Sherman Alexie's novel, The Absolutely True Diary of a Part-Time Indian.
The strong bond between Rowdy and Junior faces a significant challenge early in the story when Junior makes the difficult decision to leave the Spokane Indian Reservation to attend the mostly-white high school in Reardan. This choice is deeply resented by Rowdy, who not only refuses to join Junior but also reacts with intense anger and a sense of betrayal. He punches Junior, explicitly stating his hatred, which creates a painful rift between the two close friends.
Throughout much of the novel, Junior experiences profound loneliness and desperately misses Rowdy. Their separation is a central emotional struggle for Junior, underscoring the depth of their connection. However, despite the animosity and distance, their friendship proves resilient. The vital turning point arrives in the final chapter of the book, where their long-standing bond is ultimately healed and reaffirmed.
This reconciliation signifies the enduring nature of their relationship, demonstrating that even severe conflict and geographical separation cannot entirely break a profound connection. For a more detailed look at Rowdy's character and his relationship with Junior, you can refer to character analyses available, such as on Litcharts.
