After you file

see if you can get a letter from the custodian acknowledging that the 5498 amount is overstated.    then wait to see if you get an IRS notice about this. at that point, you can respond to the notice with the letter from the custodian which should clear things up.  if they won't provide such a letter wait for an IRS notice and explain the situation.  if the IRS does inquire please realize that it can be months or even years before this happens.