A changed synchronization shell has both a deletion in an existing mapping (DPRSystemMap) and a deletion of the schema class (DPRSchemaClass). Since the transporter tries to delete the SchemaClass object first, the DPRSchemaClass customiser throws an error because of the FK constraint violation (a relation "DPR_2426" to the DPRSystemMap). The DPRSystemMap object to be deleted is the only one that relates to this SchemaClass, so deleting the objects should work in general.
Either the DPRSystemMap object should be deleted first (but then again the relations to the DPRSystemMap object have to be considered etc.) or the check of the FK constraint should consider the objects to be deleted.