Yes, the corrected Form 1099-R must be the same as the original except have $0 in every box that on the original had a nonzero dollar amount.
I'm glad that you finally got them to see the light. That correction will avoid any issues with the IRS's interpretation of this transaction (which the IRS would have had no knowledge of had it been done correctly to begin with). What you experienced in trying to get this corrected is not unusual. Family members of mine have had the same experience that require sending emails to bank management to get the appropriate correction. Numerous people posting on the forum have had the same experience. It seems relatively universal that bank local-office personnel are inadequately trained in this area.
