Hello Daniele Cortellazzi:
I think you are referring to a known issue in KSDK with Processor Expert. This is described in the Release Notes of the Eclipse Plugin for KSDK v1.1.0:

For now the workaround is to delete all conflicting clock configurations from the CPU component. You do not necessarily need to have only 1, there may be more than 1, as long as all of them can coexist with the components timings.
We know this is a limitation and you should be able to select the clock configurations you want. So this should be fixed with the next release of KSDK v1.2, available at the end of April.
Sorry for the inconvenience.
Regards!,
Jorge Gonzalez
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