Yes, there was an exchange of ambassadorial staffs and non-combatant citizens between the US and Japan in 1942. After Pearl Harbor, American ambassador to Japan Joseph Grew was interned with the rest of the American staff. Still, previous diplomatic agreements posited that ambassadorial staffs needed to be repatriated through an exchange on neutral soil. The question was with the world at war, where could this exchange occur? After some discussion US and Japanese authorities agreed that the Portuguese colony of Mozambique was suitable for an exchange. On July 22, 1942 Ambassador Grew and 1,420 other American citizens that were living in Japan at the time of Pearl Harbor were exchanged for Ambassador Kichisaburo Nomura and 1,096 other Japanese citizens that had been interned in the United States.

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Joseph Grew wrote two books about his experiences that are worth reading if you're interested: Ten Years in Japan (1944) and Turbulent Era: A Diplomatic Record of 40 Years (1952). Grew's most famous postwar for being a public supporter of Truman's decision to drop two atomic bombs on Japan.