as FYI - a related issue with end and start date for concepts in ICD10CM is described in this forum post: ICD10CM start and end dates for retired and new concepts
Ad concept sets - I think like the phenotype group managing phenotype, having a structure of managing concept sets would be nice. A re-usable, global way to reference a concept set. In Atlas once I import a given concept set, it is not a dynamic link. By updating the linked concept set, I could update multiple phenotypes.