Description
When using the Quartus® II programmer to erase a serial configuration device indirectly using JTAG and the enhanced mode Serial Flash Loader, the serial flash might not be completely erased. The enhanced mode Serial Flash Loader is selected by default in the Quartus II programmer.
When a JTAG Indirect Configuration (.jic) file is assigned to the flash device in the Quartus II programmer, only the region of the flash that contains data in the .jic file is erased. For example, if a file containing only a 13.6Mbits FPGA image is used on an EPCS64 device, only the bottom 13.6Mbits will be erased, and the remaining 50.4Mbits will be left as is.
Resolution
If the entire serial configuration flash needs to be erased, the Quartus II programmer chain should be set up with no file assigned to the configuration flash. To do this the flash device must be manually added to the associated FPGA device: right click on the associated FPGA device and then select Edit -> Attach Flash Device, and then select the appropriate device.