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After the Millennial celebrations, as the Church in Russia began to experience more freedom from the state, Rahr began to work on the effort to reunify ROCOR and the MP. In 1990, he vehemently opposed the establishment of ROCOR parishes within Russia, which he considered to canonically be the territory of the MP. In August of 1991, Rahr and his wife were received by Patriarch Alexei II in Moscow, where Rahr brought up the subject of rapproachment with ROCOR on their behalf. Even though this attempt was rebuffed, Rahr strengthened his resolve to keep working toward this goal.
For his work with the churches, Rahr was recognized with a number of awards, from both ROCOR and the Moscow Patriarchate, including one in 1988 from the ROCOR Synod of Bishops and Archbishop [[Mark (Arndt) of Berlin]], one in 2001 from the
Polish Orthodox Church for his work in rebuilding and reestablishing the Orthodox Church at Sokołowsko, and in 2004 from Patriarch Alexei II for his life's work.