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For 16 months, the smiling faces of Shiri Bibas and her two young sons, Ariel and Kfir, had been slowly receding into the background of Israeli life as their photographs — posted on walls and bus stops soon after the family’s abduction to Gaza in October 2023 — began to fade, tear and peel.

On Friday, the Bibases’ lives and disturbing deaths were swept back to the forefront of Israel’s collective consciousness in such a startling and unsettling way that it set off fresh alarm about the long-term fate of the fragile cease-fire in Gaza. The truce looked set to continue through the weekend, as both sides prepared for another exchange of Israeli hostages and Palestinian prisoners on Saturday, but the turmoil over the Bibas family heightened doubts about an extension.

Early on Friday morning, the Israeli military announced that the body of Ms. Bibas — nominally returned, along with those of her sons, by Hamas to Israel on Thursday — appeared to be that of someone else. And an autopsy of the two boys, aged 4 and 8 months at the time of their abduction, revealed that terrorists killed them in Gaza “with their bare hands,” the military said.

A senior Hamas official, Mousa Abu Marzouq, said in a phone interview that the family was killed in an Israeli airstrike in November 2023, dismissing the accusation that a small militant group that held the hostages, the Mujahideen Brigades, had murdered them. But Mr. Abu Marzouq acknowledged that Ms. Bibas’s body may have been kept in Gaza by mistake, saying that Hamas members were now searching for her remains in a place where the family had been buried alongside Palestinians.

Neither side’s account could be independently verified.

The news set off a paroxysm of fury and agony in Israel rarely seen since the tumultuous days that followed the Hamas-led attack on Oct. 7, 2023, when up to 1,200 people were killed and 251 were abducted, including Ms. Bibas and her sons, on the deadliest day in Israeli history.