Symptoms
In the Create Document Set Wizard, after the Library has been Appified, any newly added Document set content types are not added to the selection in the Wizard. Smart Object for the list does not show added content type even though it exists on the Sharepoint List.
Diagnoses
Content types were added to a sharepoint list after creating a smart object of the list but, it was not updated in the create document set wizard in the workflow. Smart object for the list did not contain newly added content type. Forcing a regeneration of the List Smart Object would then show a newly added content type.
Resolution
Making a change that prompts the regeneration of SmartObjects will show the added document content type. This includes adding or removing a column, modifying a column's type, changing the max value of a number field, or changing the scope for people and group fields.