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The maybe notice can only be issued for a Safe Harbor Non-elective. There is no "maybe we'll match safe harbor" A Safe Harbor matching contribution can be discontinued mid-year by amending the plan to remove the match, providing 30 days advance notice of the discontinuation to the effected participants and making all matching contribution from BOY through the discontinuation in the notice. In either case a "maybe" SHNEC that is "no" or a discontinued mid year safe harbor match is not treated as a safe harbor plan for that year and is subject to ADP/ACP testing and does not get the "deemed not top-heavy" exemption if that is a concern. If the advisor is insisting they are correct, have them provide a citation but you'll be waiting a longtime to receive one.

The filing needs amending, the audit doesn't change that. Filing an amended return should not be an issue.