Please check the following steps if using the CY3686 Kit. If you are using a custom board, you can start from step 4.
1) Reset the board, it should enumerate as an EEPROM missing device with PID of 8613..
2) Now, you can open the EZ-USB interface and download the bootloader hex file onto the large EEPROM. On resetting the board it should enumerate as a bootloader with PID of 6823.
3) Now you can disconnect the device, and then open the NX2LP programming utility.
4) Once you have the utility opened, reconnect the device.
5) If the NAND Flash is not part of NAND Parts.xml, then the details of the NAND Flash can be entered into the pop-up box that comes up.
6) You should now see that it is connected to NX2LP Unprogrammed with PID of 4617. Now, on clicking the Program device button, it should program fine.
After checking this if you still have the same problem then please ensure that you have disabled the Autoprogram option. This way you will be sure the file you are pointing to is the file that is being downloaded onto the Flash. Then just try programming the flash after erasing all its contents using Ctrl+W. Sometimes, when this happens, just erasing the flash and reprogramming it usually works. If your device is being identified, but programming has failed, then it mostly points to an error in the bootloader i.e. the default.nx2 file. Please ensure that you have pointed to the correct .nx2 file.
Also please check if the pins of the Flash are all fine, as even that sometimes can cause a failure of download.
Please note that the bootloader hex file and the .nx2 file can be obtained from CY3686 Kit Contents, either with the CD or can be downloaded from the website.