A method of partially reconfiguring a field programmable gate array (FPGA) with at least one design that has interdesign routing with at least one other design programmed into the FPGA. A first configuration data set implements a first design in a first area of the FPGA, a second design in a second, non-overlapping area, and at least one bus macro that defines a bus interface between the first design and the second design. The bus interface includes a set of signal lines coupled to the first and second designs and logic that controls input and output of signals over the signal lines. A second configuration data set implements a modified version of the first design in the first area and does not implement any version of the second design. The FPGA is configured with the first configuration data set, and then partially configured with the second configuration data set.