Hi Yehuda,
Not sure if you have seen AN822 before but I think it is worth to check with you again on it.
For POF Error, it seems like the bitstream is having issue in EPCQ-A. Can you check if you have followed the migration guide such as operation codes, timing for write / read operation and etc?
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/an/an822.pdf
Meanwhile for reading operation, it seems like there is some differences in dummy clock and regenerating the s .pof, .jic, and .rpd. with EPCQ-A is required.
https://www.intel.com/content/dam/www/programmable/us/en/pdfs/literature/an/an822.pdf#page=4
Regards,
Bruce