If they said "resubmit," I would resend the entire amendment plus the missing Form 5329.
Note that when preparing an amendment with TurboTax, if you remove something that caused Form 5329 to be included with your originally filed tax return, TurboTax simply removes the Form 5329 from your tax return instead of including the Form 5329 showing the change to that form. A proper amendment includes all changed forms and schedules (except Form 1040) as is being required by the IRS in this case.
When you prepare the needed Form 5329 manually for mailing with your resubmitted amendment, explicitly indicate the change by replacing the original dollar amounts with zeros. Don't just leave those dollar amounts blank.
This answer has been verified for accuracy by an Intuit expert employee
