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Use Apply[Sequence] instead of Flatten: Manipulate[a, Dynamic@Grid[{{"Check 1", Control[{{a, 0, ""}, {1, 0}}]}, If[a == 1, Sequence @@ {{"Check 1.1", Control[{{aa, 0, ""}, {1, 0}}]}, {"Check 1.2", Control[{{ab, 0, ""}, {1, 0}}]}}, Unevaluated[Sequence[]]]}, Alignment -> {{Right, Left}, Automatic}], ControlPlacement -> ...


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