When using the Generic Flash Programmer, for the customized 'Program' operation, selecting 'Program/Configure' in Intel® Quartus® Programmer will do an 'Erase' first in addition to 'Program'.
However, 'Verify', 'Blank-Check', 'Examine' and 'Erase' in Intel® Quartus® Programmer will do corresponding flows exactly according to your definition.
To define your flash and customized flows, please refer to:
Generic Flash Programmer User Guide Intel® Quartus® Prime Pro Edition, or
Generic Flash Programmer User Guide Intel® Quartus® Prime Standard Edition.