File I-130 and a new I-485 ASAP. Your naturalization means her existing I-485 could be denied, and her EAD revoked. She should not leave the US without having Advance Parole based on the new I-485, or the green card itself.
PD: Jan 2003 (EB3 rest of world)
I-485 Approved: July 2007
I am a layman, not a lawyer. What I write here is not official or professional legal advice. In addition, my answers on this forum are specific to the scenarios discussed in each thread and should not be generalized to other situations.