The refund meter during the amendment process only shows the differences between your original return and your amended return.
Example: Your original refund was $200 before the amendment. You amend your return to include the student loan interest statement and now the refund meter shows you have a $40 refund. This $40 is in addition to the $200 you will already receive, not a replacement.
Amended returns are processed separately from original returns, so you will receive your original refund first and then your amended refund will come much later. It takes up to 16 weeks to process amended returns and they must be filed by mail.