Your 2017 tax liability resulting from the distribution of the earnings has NOT been paid. The tax withholding does not apply to any particular item that is generating your tax liability and in this case is credited on your 2018 tax return, not on your 2017 tax return. (For this reason it usually makes no sense to have taxes withheld from a return of contribution.)
Whatever additional income tax and early-distribution penalty results from the earnings reportable on your 2017 tax return WILL need to be paid with your amendment. The taxes withheld, credited on your 2018 tax return, will simply decrease your 2018 balance due or increase your 2018 tax refund and will have no effect on your 2017 amendment.
