Benoît Peeters's biography "Derrida" (Polity Press, 2013) contains a short description of the reconciliation of Jacques Derrida and Jürgen Habermas in 1999-2000:
"As he grew older and the thought of death obsessed him more, Derrida seemed eager to come to a rapprochement with some of his former adversaries. In October 1999, in New York, he again met Jürgen Habermas at the home of their common friend Giovanna Barradori. At this unexpected encounter, Habermas had the ‘smiling kindness’ to propose that he and Derrida hold a discussion. Derrida accepted immediately: ‘It’s high time,’ he said, ‘let’s not wait until it’s too late.’ The meeting took place in Paris shortly afterwards. During a friendly lunch, Habermas did all in his power to ‘wipe out the traces of the previous polemic, with an exemplary probity’ for which Derrida would always be grateful. The two men had not been on good terms for over twelve years, because of the two ‘unfair and hasty’ chapters that Habermas had written on Derrida in The Philosophical Discourse of Modernity and Derrida’s stinging response in Mémoires: For Paul de Man and Limited Inc. [......] For Derrida, the quarrel with Habermas had had serious consequences: since the mid-1980s, access to the most important German publishers had been blocked, and his influence in the German-speaking world had been greatly hampered.
Their rapprochement was initially brought about on political terrain. Even during the years when they had been at odds, they had frequently been signing the same petitions and the same manifestoes. Derrida later acknowledged this in a fine homage that he wrote for the seventy-fifth birthday of his former enemy: ‘I had always had more than just sympathy, but an admiring approval for the argued positions that Habermas had adopted in Germany itself, on problems in German history, on numerous occasions.’
In 2000, Habermas and Derrida organized a seminar together in Frankfurt on problems in the philosophy of law, ethics, and politics. Alexander García Düttmann remembers the disquiet that this ‘reconciliation’ spread among the disciples of the two philosophers. ‘This rapprochement irritated me. Philosophically, they had nothing to say to one another. But politically, okay, they agreed on several points. Also, we shouldn’t underestimate tactical considerations. Derrida could be very trenchant, but he could also be a skilled negotiator when the occasion called for it. Depending on the context, he could be radical or almost consensual, courageous or calculating.’ Avital Ronell confirms that this episode caused their respective associates some heart-searching: ‘One could write an entire history of great men or women [. . .] and their disciples, a history of associations or dissociations, of gravitational pull. [. . .] Small groups quarrel and suddenly their leader, Mafi alike, perhaps, proposes a truce.’ One thing is certain: making up with Habermas meant that Derrida quickly reassumed a position in Germany that he had lost. Several plans for translation and re-publication saw the light. But other factors also helped to thaw the situation. After many years spent in the United States, Werner Hamacher, a follower of Derrida, had returned to teach in Frankfurt in 1998; he soon invited Derrida there, to give the lecture ‘The university without condition’. On this occasion, Derrida met up with Bernd Stiegler – not to be confused with Bernard Stiegler –, who had attended his seminar in Paris a few years earlier and now had an important position with the great publisher Suhrkamp. The Adorno Prize would soon seal Derrida’s reconciliation with Germany." ["Derrida", p. 501f].
In 2003 Jürgen Habermas and Jacques Derrida published together "A Plea for a Common Foreign Policy, Beginning in the Core of Europe".