I'm using EE2007.8, in the DxDesigner I defined swappable pins in a BGA, all tests passed successfully.
After swapping some pins in the layout stage, I did back annotation and forward annotation, but when running the packager I get errors (an example is below):
ERROR: Connectivity error in CES configuration - does not match Flat configuration:
Physical net "FPGA_WDO" is incorrectly connected to CES pin UID=(1463,702,52). Flat net "FPGA_WDO" has no corresponding connection.
I didn't find any problem in the schematics; it seems the CES wasn't updated with the swapping.
It also seems that cross probing from the schematics to CES of those specific nets don't work.