It seems that you will have no choice but to file a substitute Form 1099-R (Form 4852) if the custodian refuses to report the distribution as a return of contribution. You apparently already have a code-4 Form 1099-R for the distribution from the 401(k) which is taxable, so you don't want to get taxed twice on the same money. Only any investment gain while the the funds were in the IRA is taxable on the distribution from the IRA. The Form 4852 will provide a place to add you explanation of the circumstances.
