The Paraller Flash Loader II Intel® FPGA IP (PFLII IP) will first check if CONF_DONE is low. The IP will not proceed with configuration if it is already high. This is why the PFLII IP cannot configure Intel® Stratix® 10 devices.
Check if CONF_DONE is pulled up as CONF_DONE and INIT_DONE are no longer required to be pulled up to VCCIO_SDM.
Note that SDMIO_0 and SDM_16 are initially pulled down. Hence an intermediate voltage level by pull-up and internal pull-down resister might cause configuration failure when using the PFLII IP.
PFLII IP monitors CONF_DONE signal low as start condition of operation. This requirement has been changed for Intel® Stratix® 10 devices.