Cypress NAND flash might not be recognized by Cyclone® V SoC FPGAs if you have followed the Cyclone® V GX, GT, E, SX, ST and SE Device Family Pin Connection Guidelines, which recommends connecting NAND_RB through a 1KΩ -10KΩ pull-up resistor to VCCPD_HPS.
For Cypress NAND flash, it is recommended to connect NAND_RB through a 10KΩ -50KΩ pull-up resistor to VCCPD_HPS.
The Cyclone® V GX, GT, E, SX, ST and SE Device Family Pin Connection Guidelines will be updated with this information in a future release.