If an RPD file contains only configuration data, why does Quartus generate differing RPD files for EPCQ and EPCQA devices? Shouldn't they be identical?

Hi Mark, The reason is dummy clock, Actually dummy clock is configurable in EPCQ devices but it`s fixed in EPCQ-A devices so the files generated by Quartus such as .pof, .jic, .rpd are different for EPCQ & EPCQ-A devices. Refer the page 4.of AN822, https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/an/an822.pdf Let me know if this has helped to resolve your issue. Regards, Vikas