The IRS MOST LIKELY will refund the $1,491 (the second payment you made plus the 91 refund) but it might take a bit of time.
You should expect a letter from the IRS explaining your next steps.
You MAY need to amend a second time to get that 1,400 back, but as I say, most likely they will adjust your original return and then the amended return as well.
You might check the IRS Your Online Account to see what the IRS has listed.
IRS Your Online Account
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