Disclosed approaches for processing a circuit design include identifying duplicate instances of a module in a representation of the circuit design. A processor circuit performs folding operations for at least one pair of the duplicate instances of the module. One instance of the duplicates is removed from the circuit design, and a multiplexer is inserted. The multiplexer receives and selects one of the input signals to the duplicate instances and provides the selected input signal to the remaining instance. For each flip-flop in the remaining instance, a pipelined flip-flop is inserted. Connections to a first clock signal in the remaining instance are replaced with connections to a second clock signal having twice the frequency of the first clock signal. An alignment circuit is inserted to receive the output signal from the first instance and provide concurrent first and second output signals.