Short version of this: the concepts that are members of a ValueSet aren’t directly related to the ValueSet. The canonical URLs for the ValueSet would only be mapped to the ConceptSet itself… The concepts themselves have an independent identity (in FHIR terms, concepts belong to a code system). So it’s perfectly valid to have a ValueSet that’s, e.g., “all the codes in http://terminology.hl7.org/CodeSystem/v3-substanceAdminSubstitution except TE”. That’s a different ValueSet than the http://terminology.hl7.org/ValueSet/v3-ActSubstanceAdminSubstitutionCode, but it uses mostly the same members, so, e.g., the EC code is still (canonically) http://terminology.hl7.org/CodeSystem/v3-substanceAdminSubstitution|EC in both the standard ValueSet and the customised one; it’s just that, e.g. http://terminology.hl7.org/CodeSystem/v3-substanceAdminSubstitution|TE is a value in the canonical value set but not the customised one I’ve defined.
Does that make some kind of sense? I.e., the URLs that refer to the concepts are not affected by the ValueSet URLs at all.