Due to a problem starting with the Intel® Quartus® Prime Pro software version 18.0, if your Intel® Stratix® 10 device is first configured via JTAG, you can't subsequently reconfigure via a non-JTAG source.
Device Family: Intel® Stratix® 10
Intel Software: Quartus Prime Pro
Last Modified: May 14, 2018
Version Found: v18.0
Bug ID: FB: 544330;
IP: Altera Config Debug Agent