From ISE software 12.2 forward, Numonyx J3 (Rev D, F) will no longer be supported for indirect programming on Virtex-6 FPGA.
The reason for removal is voltage mismatch.
J3D/F - min 2.7V
Virtex-6 Max VIN=2.65V
This part is legacy, not recommended for new designs. This BPI flash is not a good solution match for Virtex-6 FPGA since it would require multiple level shifters to be guaranteed versus other available solutions.
ISE software 12.1 sees the introduction of Indirect programming support for theS29GLxxxP.