The current RocketIO Wizard will allow line rates of only up to 5Gb/s while the -2CES9988 are qualified to run at up to 6.5Gb/s under certain conditions. This Answer Record discusses what must be done to correctly generate wrappers for these higher line rates.
In CORE Generator, it is recommended that the part selected in the project settings matches the part that will be used. Unfortunately, there is no differentiation between a normal -2 part and a -2CES9988. The result is that the RocketIO GTX Wizard will not allow you to use any line rates above 5Gb/s. To work around this, the supported method is to change the CORE Generator project settings to a -3 part, which will then allow the Wizard to generate the correct line rates.
You should refer to the -2CES9988 errata for supported use cases at line rates above 5Gb/s. That document can be found here: