Just watched 16x13 of NCIS...here’s a theory.
Ziva is in Paris with Tony and Tali. When McGee called Tony to tell them what they found in Ziva’s hideout, he then told Ziva which led her to come back and get the letter from the journal and leave the letter for Ellie. She knew the case was going to break and wanted to have the chance to read him the letter herself.
Because since she’s WITH her family in Paris, she doesn’t want anyone finding out she’s alive and putting a target on her back, hence her writing the letter to Ellie.
My theory is that she staged her own death to make everyone stop looking for her so she could be with Tony and Tali (and safely at that). I still don’t know where I stand on whether Gibbs and McGee know she’s alive, only because of the raw emotion we saw when Gibbs was yelling at Bishop.