A veteran State Department diplomat and longtime Pakistan expert is under federal investigation as part of a counterintelligence probe and has had her security clearances withdrawn, according to U.S. officials. The FBI searched the Northwest Washington home of Robin L. Raphel last month, and her State Department office was also examined and sealed, officials said. Raphel, a fixture in Washington’s diplomatic and think-tank circles, was placed on administrative leave last month, and her contract with the State Department was allowed to expire this week. Two U.S. officials described the investigation as a counterintelligence matter, which typically involves allegations of spying...