The Quartus® II software may be configured to generate an SVF file by checking the appropriate option in the Assignments -> Device -> Device and Pin Options... dialog box.
If an Arria® II GX device with Active Serial configuration is configured using the Quartus II programmer or a third party boundary scan tool using an SVF file that is generated this way, then the attached Serial Configuration Device will no longer be accessible using the altasmi_parallel Megafunction or the Serial Flash Loader (SFL) IP.
Generate the SVF file using the Quartus II programmer software as described in the related solution below, instead of via the Device options available for Quartus II Assembler.