Using the remote system upgrade feature allows connection of a Cyclone® III device to a serial or parallel flash configuration device. The configuration device can be loaded with a factory image and one or more application images. At power up the known good factory image is loaded and the part goes into user mode. At some time in the future the users application can detect a new application image and trigger the device to reconfigure. If the configuration finishes without error the device goes into user mode again with the new image. If there is a problem during this process, the controller will automatically revert back to loading the known good factory image so there is zero down time.