If done by direct rollover, the transaction is nontaxable and not subject to withholding, so it's unclear to me why reporting on Form 1042-S would have been necessary.
I would probably submit a substitute Form 1099-R with which you can supply explanation. Assuming a direct rollover, the code for Form 1099-R box 7 is G and the taxable amount is zero. Unless something has changed to allow a tax return with a substitute Form 1099-R to be e-filed, doing so would require printing an mailing your tax return.
