Hi Herve,
Processor Expert components in KDS1.1 and KDS2.0 are not compatible. As Iva said, the best way is to create a new KDS2.0 project and copy all your source files, unfortunately you will need to configure your components again and there is not a simple way of porting them by the moment.
I dont see any problem using PEx and KSDK. If you select both option the PEx components for KSDK will be enabled. If you dont select KSDK then the classic LDD driver will be enabled. Note that you will not be able to use the classic LDD drivers if you select KSDK.
You can find PEx Issues and Limitations in the Release Notes:
C:\Freescale\KDS_2.0.0\eclipse\ProcessorExpert\PEx_KDS_2_0_0_Release_Notes.pdf
If you have any question please let me know.
Regards,
Carlos
Technical Support Engineer