The quartus_hps tool erases both the factory NAND bad block markers and the software maintained bad block tables. This can lead to unreliable NAND operation. Symptoms include intermittent or permanent failure to boot from NAND, failure to configure the FPGA from the HPS using NAND and also NAND CRC errors.
To work around this problem, use U-Boot or Linux to program NAND memory.
Note: U-boot can be loaded via the Arm DS-5 Altera Edition debugger, or from FPGA on-chip-ram, and the HPS ethernet or the debugger can be used to transfer the NAND Image to SDRAM for use by u-boot for programming.
This problem is scheduled to be fixed in a future release of Quartus.