Why am I unable to regenerate my EDK system after making modifications to the ChipScope core?
There is a problem with the supporting files for the ChipScope core.
To work around this problem, the EDK design needs to be "cleaned" of all netlists and the design will need to be completely regenerated.
This problem has been fixed in the latest 10.1 Service Pack available at:
http://www.xilinx.com/support/download/
The first service pack containing the fix is 10.1 Service Pack 3.