The $assemble operation should import all the contain value sets declared in sub questionnaire to the assembled questionnaire. Without those contained value sets, item.answerValueSets in sub questionnaire will have invalid reference.

Example: gender value set used in Patient information questionnaire

        {
          "linkId": "PBD.5",
          "text": "Gender",
          "type": "choice",
          "answerValueSet": "#gender"
        },

Also extensions declared in sub questionnaire, such as CQL library, need to be merged/imported during assemble operation. CQL questionnaire could not calculate result without library extension.