If the miles are legit (e.g. not as a result of a second attempt to collect bonus miles for signing up for a SkyMiles AMEX), then a simple e-mail explaining the situation should suffice. Of course, now that the duplicate account is closed you won't be receiving the miles for the magazine purchase. I'd nicely ask them to credit your main account for that purchase as well given that it was done only because the account consolidation was not done in time.