A method of modeling two IC dies using the same software model, although the two dies include physical differences. A first programmable logic device (PLD) die includes first and second portions, and is encoded to render the first portion operational and the second portion non-operational. At a boundary between the two portions, interconnect lines traversing the boundary include a first section in the first portion and a second section in the second portion. The second PLD die includes the first portion of the first PLD die, while omitting the second portion. The interconnect lines extending to the edge of the second die are coupled together in pairs. A software model for both die includes a termination model that omits the pair coupling, adds an RC load compensating for the omitted connection, and (for bidirectional interconnect lines) flags one interconnect line in each pair as being invalid for use by routing software.