We had a nice discussion 6 of March work-group and finalized the decision:
For a HCPCS and CPT4 concepts deprecated because of the source withdrawal, we make the Standard_concept = 'S' and invalid_reason = null, but valid_end_date reflects the withdrawal date.
This makes possible to use these concepts as standard and fill up the CDM, and also CDM builders can easily check the consistency of the data ensuring that event date is between concept's valid_stard_date and valid_end_date.
Once we have resources available, we'll implement these changes
Note, we make this for HCPCS and CPT4 only. In the future we'll analyze the other vocabularies, understanding why the source deprecates the concepts and then we'll make a decision whether we need to deprecate them or just change the valid_end_date but not affect Standard_concept and invalid_reason values.