This exact problem has been addressed in this forum many times, but the forum search function is relatively inadequate for finding relevant posts.
By depositing the pre-tax funds into the Roth IRA, it became an irrevocable conversion. As long as you put a zero in box 5 of TurboTax's 1099-R form and indicate to TurboTax that the entire amount was rolled over to a Roth IRA, TurboTax will treat the distribution as fully taxable despite the zero in box 2a. If you want to make it more explicit that the distribution is taxable, you can enter and file a substitute Form 1099-R (Form 4852) showing the correct taxable amount in box 2a and providing explanation that the rollover was deposited into a Roth IRA instead of into a traditional IRA.
This transaction has nothing to do with Form 8606.
