It appears that you reported everything correctly. It seems that the IRS jumped the gun on generating the letter, or an IRS examiner involved is inexperienced.
The IRS is aware that a code R Form 1099-R is not issued until about a year after the due date of the tax return reporting the recharacterization, so the IRS normally does not question such a recharacterization if you provide proper explanation (and the corresponding code R Form 1099-R is eventually received by the IRS). The IRS might question the recharacterization if you did not provide in your explanation the date of the conversion and the date of the recharacterization, perhaps causing the IRS to believe that the recharacterization was performed in the same year as the conversion and causing them to expect to receive a code N Form 1099-R instead.
