To resolve this issue, perform the following:
- Open the ISE project in ISE 11.1 and migrate it if this has not already been done
- Remove the EDK project (XMP file) from the ISE project
- Open the XMP file in EDK (Xilinx Platform Studio) standalone and update all the cores using the Wizard
- Close EDK (Xilinx Platform Studio)
- Re-add the XMP project file to the ISE project by going to Project -> Add Source...
After you have completed this process, you should be able to use the EDK project within the ISE project as before without any problems.