You can program the CFI Flash device without reprogramming a MAX® II device which already has the Parallel Flash Loader (PFL) IP in it, by enabling both the DO_BYPASS_CFM and DO_BYPASS_UFM procedures, when executing the .jam or .jbc file.
For example, if using the quartus_jli executable,the command would be :
quartus_jli -c1 -aprogram -eDO_BYPASS_CFM -eDO_BYPASS_UFM filename.<jam/jbc>
If using the JAM STAPL player, the command would be :
jam -aprogram -dDO_BYPASS_CFM=1 -dDO_BYPASS_UFM=1 filename.jam
The Jam STAPL Byte-Code (jbc) Player uses the same command as above to run a .jbc file, except for the
executable name.