Description
No. When the Intel® Quartus® Programmer examines the EPCQ/EPCQ-L/EPCQA configuration devices, it doesn't read the non-volatile configuration registers (NVCR). So the examined programmer object file (.pof) doesn't have the NVCR values.
If you program a configuration device with such .pof, the Quartus Programmer will use the value read from the current configuration device.