When you file your 1040x, it is treated as a separate tax return which means that any refund that it states you are due will be sent to you in the method you select when you file the 1040x. The refund that was sent with your original return was for that return and is not expect to be paid back.
If when you file the 1040x, and there is a refund, you will receive that refund. If there is a balance due, you will be expected to pay that.
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