When MAX® II and MAX V devices are reprogrammed using a JAM file where Real-Time ISP has been enabled, the configuration RAM of the MAX device is not updated following programming and the device will continue to run from the existing configuration.
To enable reconfiguration of the MAX device following reprogramming, the optional procedure DO_FORCE_SRAM_DOWNLOAD must be used. For example this command could be used:
quartus_jli -c <cable> <JAM file> -a PROGRAM -e DO_FORCE_SRAM_DOWNLOAD