When using the Nios II Flash Programmer (now "quartus_pgm --nios2") with the Serial Flash Controller II IP in a design, a new option "--csr" is required to be specified in the command string.
The --csr option should be specified with the address of the "avl_csr" interface of the Serial Flash Controller II IP core. For example, in a Platform Designer system where the address span of the "avl_csr" interface is 0x1000_0000-0x1000_003F, use "--csr=0x10000000".
This feature is expected to be fully documented in a future version of the Nios II Flash Programmer User Guide.