Hi SirenDoll, and thanks for the response.
Well, we already arrived on January 12, and she was admitted through the Visa Waiver Programme. The thing is that I was under the impression that once she had her interview and received her citizen certificate, I wouldn't have to leave the country (they would adjust her status through her I-94 number somehow). I applied for the N-600k then we were living abroad but we moved now in January to permanently stay, another thing is that initially she did not qualify (since I did not live in the US after the age of 14) for CRBA.
Leaving and entering the US is not a big issue for us since we are in Puerto Rico and can easily travel to DR and back in order to get her maximum stay duration renewed.