While Reference Questionnaires cannot be edited once published, there is a way to edit questions in the reference question library.
Warning: Do not make substantial edits that would change the meaning of past answers.  This fix is for minor edits only!
To update a question on a published Reference Questionnaire:

1. Navigate to Opportunity > Evaluators > Questionnaires
2. Click the green Edit button next to any drafted questionnaire. If no drafted questionnaires are available, create a new one.  To keep a drafted questionnaire for this specific purpose, you can name it "Keep as drafted - Do not use" or similar.
3. Select the Questions tab
4. Click the Add Reference Question button
4. Locate the question to be edited and click the Details button on the right
5. Make the desired changes
6. Click the green Update Question for All Opportunities button.  This will update the question on all opportunities and applications, archived and unarchived, it has been used on.