Other than hoping and praying? You could try to submit the 1040X electronically (capability was introduced this summer), but that may complicate things further. If they see two, they have to investigate and reject one, making the entire process longer. If they never see the paper one, the electronic one will be processed, but there’s just no way to tell or predict things will happen this way.
My experience: the electronic amended return was processed with a check in my hand right at 16-17 weeks.
