Normally the retirement account would file Form 990-T to report the UBTI and pay the UBIT. If the trustee of the retirement account requires you to prepare the Form 990-T, that would require coordination with the trustee of the account. Did Form 990-T not get filed and the IRS ended up assessed the tax and took funds from the retirement account to pay the UBIT? The IRS "withdrawing" funds from the account under these circumstances would not be a distribution and would not be reported on Form 1099-R.
