It was a very short fanfic, less than 10 chapters I think and it's not finished / barely started.
All I remember is that Hermione found out that she was expecting Harry's child during the war, so she left the Wizarding World to protect her unborn child without telling Harry. She came back around three years later.
If I remember correctly, Hermione named the child Emilia Lilianna Granger, or something along the lines of that. The fanfic stopped at that part.
I read the fanfic either in quotev or fanfiction.net or some kind of harry potter fanfic site.