Online Community of Zenith Builders and Flyers
I would definitely NOT contact the FSDO as a first step. Unlikely to get anything except a regulatory based response. Once done, very hard to get back to square one and fair, uncluttered territory on this matter.
First - Reconstruct as much history of the build as possible. Zenith sold the kit. When? To Whom? Talk to the seller and go backwards in time to the original builder. Contact and inquire of everyone on the trail, including any local EAA chapter or other parties along the way. For example, where the aircraft was built may provide people and photos who know the fact.
Treat the history like a detective novel and piece the story together. Collect names, dates, and even "witness" statements. All details matter.
Second - Seek out, with all that research in hand, a known and supportive DAR who will fairly consider all the facts. A DAR who is understanding and supportive can make all the difference here.
From the second link: Forget about the FSDO and the MIDO, find a DAR who will cooperate with a rebuild and recertification. --- Your friend's situation is loads better than this case as it is a fresh, no previous Airworthiness Certificate aircraft.