I believe the lost two has something to do with the 3 Knights in the Secret Ending and some events that takes place during and before Kingdom Hearts 2. In the Final Mix+ cutscene in Hollow Bastion, it reveals Xemnas going down the hallways in the secret corriodors of Hollow Bastion and typing in pass words.
As he reached the final floor and set in the chair, which unlocked another passage way, as the camera turns around we see the FS's armor and Keyblade. Obviously her body is not there. I consider her lost.
Sora, Donald, and Goofy arrived in Disney's Castle and goes through a darkness corridor that takes them to the world I would call "Sunsets Horizon". As the sand storm blew over, the ES was there sitting alone with his Keyblade. Notice that he is by himself and not companied with his friends. Perhaps the BHS and the FS were lost during his story and his quests involving the Keyblade(s), Xehanort, (ect).