Over the past decade, the steady growth rate of FPGA device capacities has enabled the development of multi-FPGA prototyping environments capable of implementing millions of logic gates. While software support for translating new user designs from gate and RTL-level netlists to FPGA bitstreams has improved steadily, little work has been done in developing techniques to support the translation of incremental design changes at the netlist level to a set of replacement bitstreams for a small number of FPGAs in a multi-FPGA system. As system sizes and design compilation times increase, the need to support rapid, incremental compilation grows progressively important. In this paper we describe and analyze a set of incremental compilation steps, including incremental design partitioning and incremental inter-FPGA routing, for two specific classes of multi-FPGA emulation systems. These classes are defined by the techniques that emulation software systems use to determine inter-FPGA communicat...