A graphical tool assists a user in migrating programming changes from one programmable logic device to another. The tool preferably compares a new user configuration dataset (e.g., the user configuration dataset including old features as well as newly-added features) for the "origin" programmable logic device to the existing user configuration dataset (i.e., the user configuration dataset including only old features) for a "destination" programmable logic device, and displays differences to the user. The tool preferably also assists the user to synchronize the devices by "copying" the new features of the user configuration dataset for one device into the old user configuration dataset for another device to the extent possible, by providing graphical inputs to allow the user to indicate which features should be synchronized, or to graphically manipulate the feature assignments directly.