When you begin amending a tax return, one of the first things that happens is that the program assumes that you received your refund (which is why we recommend waiting until you actually receive it). So it zeroes out your refund, and any changes that you make with an amended return will result in either an additional refund (if you're increasing expenses) or a balance due (if you're reporting more income or reducing expenses.

You really should wait until you receive your refund to make sure that you are starting your amended return from the correct point.