Create a 'JTAG Indirect Configuration' (.jic) file.
Refer to the "Generating .jic and .jam Programming Files in the Quartus II Software" section of AN-370 - "
using the altera serial flash loader ip core with the quartus ii software (
https://www.altera.com/content/dam/altera-www/global/en_us/pdfs/literature/an/an370.pdf)". You will have to specify a suitable .sof file to create it. However, given what you're doing it'll be ignored.
Once you have opened this file in the Quartus programmer, you can choose to erase the EPCS attached to your FPGA.
Cheers,
Alex