There may be no problem ... it doesn't always go to zero. Ignore the refund meter when amending the return ... instead review the 1040X itself ...
Look at the form 1040X …
Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.
If you completed it correctly you will see an entry on either line 16 OR 18:
On line 16 should be the amount you paid with your original return. If you paid nothing already then this line should be zero.
On line 18 should be the amount of your original refund you received. If you have not received your refund yet then you need to wait for it. If the refund changes from what you expected then this line must reflect that change.
Then you will see your extra refund on line 22 OR the new balance due you need to pay on line 20.