i think you have 30 minutes after train has left.. I saw something like that somewhere.. and then you pay the difference of your ticket and new fare if there is any. go directly to customer service NOT THE TICKET OFFICE: Let them direct to the ticket office if needed.

I wonder if the Rail Desk at Madrid Airport can do what a ticket window at Atocha can do - could do it earlier.???

What time is the next flight from Barajas airport to Seville airport after your arrival? And, how much does it cost?

Is it a reasonable alternative to the train?

Is there still a full-service rail desk at the airport as I used several years ago- that can book tickets - change tickets, etc -

if so I'd think of just buying a full-fare ticket once in Malpensa for the next leisurely available train from Atocha to Seville- or gamble on a discounted ticket if cheap enough and then if miss it just buy another full-fare ticket at airport rail desk where lines when I were there were short and folks spoke good English.