A code-4 Form 1099-R with you as the payee is an assertion by the custodian that the payment was made to you and that's what you need to refute. The determining factor is who or what was the actual payee on the payment made by the old custodian. If the payee was you, this was an impermissible rollover. If the payee was your new IRA (or new custodian) FBO you, it's a nonreportable trustee-to trustee transfer as long as the new custodian deposited the money directly into the new inherited IRA. You would want to obtain documentation from the old custodian that indicates the payee of this payment. (If you did not have to endorse any check made out by the old custodian, presumably the payment was not made to you.)
There is a Written Determination (PLR 200204048) made by the IRS to a non-spouse beneficiary who asserted that a series of partial of transfers of an inherited IRA to several new custodians were trustee-to-trustee transfers and were not taxable, but later when the IRS received information that the beneficiary received a Form 1099-R from the original IRA custodian they revoked the original determination and made a new determination (PLR 200228023) that that transaction was a taxable distribution that was not eligible for rollover. This suggests that the IRS gives greater weight to the assertions of the old custodian than they do to the assertions of the beneficiary (absent any documentation that contradicts the assertion of the old custodian).
