Shasta Groene's 9-year-old brother, Dylan, remained missing and was feared dead, Kootenai County Sheriff's Capt. Ben Wolfinger said.
"Our initial information is that he may be deceased," Wolfinger said, adding that officials were continuing the search for him. He would not elaborate on what kind of information investigators had.
Joseph Edward Duncan III, of Fargo, N.D., was charged with kidnapping and was being held without bond, Wolfinger said. He said more charges could be added.
Authorities are looking into whether Duncan, 42, had a role in the three killings May 16, he said.
Shasta Groene was spotted in her hometown by a waitress who apparently recognized her from photographs in the media.
Shasta seemed well, and was being interviewed by investigators at a medical center. Her father was on his way to Coeur d'Alene to be reunited with her, a relative said.
"She was sitting in a restaurant eating a meal. She's obviously well enough to do that," Wolfinger said.
Authorities do not yet have information about where the girl had spent the past six weeks, he said.
"She's a little girl," Wolfinger said. "Obviously she's been through a pretty traumatic time."
The child's father, Steve Groene, was reported to have returned from visiting relatives in Tacoma, Wash., he said.
Duncan was driving a red 2005 Jeep Grand Cherokee stolen in St, Paul, Minn., on May 4, with stolen plates taken April 27 in Newton County, Mo., Wolfinger said.
Police were seeking a warrant to search the vehicle.