"leave me with a refund due" - your original return had a sizable amount due, but when you filed the extension, that amount you paid with the 4868 changed it to a refund. So that is OK, too.
Yes, I had thought that a 1040X should start with a zero refund or amount due, but in the case, TurboTax is making a number of changes before you even start. The changes are all correct, just puzzling.
Give it a try.
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