Traditional IRA basis but $0 balance

[user17693542199]

In 2022 I made a nondeductible contribution to a rollover IRA. In 2023, I rolled over the whole rollover IRA into a 401k, zeroing it out the rollover IRA. I then did a backdoor Roth by contributing to a new traditional IRA and converting it to Roth. I now realize that my tax returns are showing I still have a basis in traditional IRA even though all my traditional IRA accounts are $0. 

How do I fix this?

[dmertz]

Basis in nondeductible traditional IRA contributions is not permitted to be rolled over to a 401(k).  Only pre-tax amounts are permitted to be rolled over to a 401(k).  Your options are

1. Get the 401(k) to make a corrective distribution of the basis from the 401(k).  You could then perhaps do a late rollover of that amount to a Roth IRA as a conversion under IRS Revenue Procedure 2020-47, amend your 2023 tax return to reflect that Roth conversion (two Roth conversions in 2023), eliminating the carryforward of the basis or,
2. Same as #1 except do the late rollover to a traditional IRA, perhaps avoiding the need to amend the 2023 tax return or,
3. Ignore the mistake, correct the basis carried forward to your 2025 tax return be $0 and pay tax again on this amount when eventually distributed from the 401(k).   (Mistakenly rolling basis over to the 401(k) does not create after-tax basis in the 401(k).)  Or,
4. Retain the basis carried forward and, when you are eligible to take distributions from the 401(k), do an ordinary rollover from the 401(k) to a traditional IRA.  However, I don't know that this  would pass scrutiny under an IRS audit.  When you rolled the finds to the 401(k) you effectively certified that it contained no after-tax basis, so this would seem to mean that you gave up that basis.

Given that the mistake was made in 2023, you might have a tough time getting the 401(k) plan to make a distribution now and #3 might be your only viable option.