After you file

You will need to delete your Form 8888 to e-file your amended tax return. 

First of all you should not e-file your amended return until you receive your refund. The amended return is processed separately from your original return, it doesn't "catch up" with the original return. You will still receive the original refund and you will need to pay back the difference. 

To delete Form 8888:

1. Open your return by clicking on Fix my return.
2. Scroll down to Tax Tools on the bottom of the left side menu.
3. Select Tools.
4. Click on Delete a form (third on the list at the bottom of the screen).
5. Find Form 8888 on the list of forms.
6. Click Delete to the right.
7. Confirm your Delete.
8. Click Continue in the lower right. 
9. Click Continue with my return.
10. Click Continue to file and resubmit your return.