If you need to change a questionnaire in mid-cycle (which you should try to avoid whenever possible) what you should do will depend on what is to happen in the applications that have already submitted that questionnaire.
If you need everyone to resubmit the questionnaire and you don't need to retain the previously submitted responses, you would retire the existing questionnaire (and remove it from the application cycle process map) and create a new one. It will make the previously submitted questionnaires disappear from the applications and the new one will appear to all applicants.
If you want to keep the responses that had been previously submitted but deploy a revised version of it to new applicants, you will just want to edit the existing questionnaire and deploy the new version out to the app cycles. That will retain the previous version's submissions in the applications that already submitted it.
Important: In both cases, it is recommended to run a report to export the questionnaire data that has already been submitted for the questionnaire BEFORE you implement the change. The old version's submitted data may no longer be accessible through the reporting tools after retiring/updating the questionnaire.