Hi Frédéric,
If you don't ever plan to use PE for the BSP, just delete the .pe file from the new BSP.
If you wish to add it, it might be more difficult. As far as I know it doesn't allow to just open the PE file and change the processor type from K60 to K20 at the moment. Therefore, I would suggest to delete the original .pe file, then use CodeWarrior menu to add PE support for an existing C project (select the BSP project and File->New->Other... then under Processor Expert select "Enable Processor Expert for Existing C Project"). Then, the PE in the BSP project should be configured to not generate "main" function (as there already is one main() function in the BSP) and I would recommend to disable "Generate Processor Expert code before build"). If you wish to use PE to generate code for the BSP, it needs be configured to generate code for the clock module (see /doc/tools/cw/Howto_SetupKinetisClock_UsingPE.pdf).