In chapter 7 of Avi's The Man Who Was Poe, it is while Edmund sits by the fire in Mrs. Whitman's kitchen, eating bread and jam, that Edmund prayerfully and emphatically says to himself, "Sis is alive. . . She is alive" (65). Edmund's certainty that she is alive stems from hopeful thinking and his own intuition.
In chapter 3, Edgar Allan Poe, calling himself Mr. Dupin, notices that the window of Edmund's tenement flat is near enough to the window next door that one can reach out and touch the other window. In chapter 5, they manage to gain entrance to the room, where Dupin finds a "wooden plank leaning against the wall near the window through which, just across the way, they could see Edmund's room" (45). Dupin discovers the plank easily reaches both window sills, making a perfect bridge for someone to walk from one window to the other. In this same chapter, Edmund finds a "pearl button" on the floor of the room, a button he knows came from his sister's shoe. Edmund also explains that Sis's favorite story is "Hansel and Gretel," and Sis must have left the button intentionally, just as the children in the story left a trail of crumbs. Dupin deduces that Sis has been kidnapped.
It's also at this point in the story that the motive for the kidnapping is being hinted at—the Providence Bank has just been robbed of a gold deposit. Everywhere Edmund goes that day, he hears talk of the gold robbery, including in the clothier's and Mrs. Whitman's kitchen. While hearing about the robbery, Edmund must have intuitively deduced the robbery and his sister's kidnapping are connected, and if she was kidnapped for the purposes of the robbery, then chances are she's still alive, as she may have been used in the robbery in some way.