You are correct that you are allowed to withdraw $22,000 per disaster.
In order to do this in TurboTax you have to enter two separate 1099-Rs. After you enter the first it will ask you for all of the information about the federally declared disaster that you pulled the money out for. After you enter the second one it will pre-fill the disaster for you with the same disaster information that you entered for the first disaster.
You need to overwrite the disaster information that the system has pre-entered for you and enter all of the information for the second qualifying disaster. This should allow you to remove the early withdrawal penalty and spread both out over three years.
@jhvanden
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