You can use quartus_jli and a .jam file generated from a .JIC file to unprotect the block protect bits in an EPCS or EPCQ configuration devices. The generated .jam file will contain the appropriate programming algorithm for this procedure.
If using the quartus_jli executable, the command would be:
quartus_jli –aPROGRAM –eDO_EPCS_UNPROTECT <filename>.jam
If using the JAM STAPL player, the command would be:
jam –aPROGRAM – dDO_EPCS_UNPROTECT=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.