The earlier hearing had failed to provide a plausible and cogent explanation for Thongsi's death, she said today, and therefore she wanted to recall some witnesses who might face "confronting and uncomfortable" questions.
"This is an unusual step and not one I have taken lightly," Windley said.
An interim non-publication order prevents naming some witnesses and reporting other details of the case.
Two men on the dive trip have given conflicting accounts of what happened during the fateful event.
Thongsi had dived into the water from a boat off the Motunau coast.
She resurfaced after her spare regulator was leaking some air.
The skipper, an experienced diver, pushed the regulator a few times which he says appeared to fix it, the inquest heard.
Another member of the dive party helped Thongsi as the skipper returned to the wheel of the boat.
But as Thongsi went back below the water's surface, witnesses' versions of events differ.
The skipper thinks she was breathing as she went back under, and saw bubbles emerge.
However, another man described her as showing no signs of life, looking through him, and sinking straight down.
Those varying accounts were hard for Windley to reconcile.
When there were no bubbles seen on the surface, the skipper today said he grabbed a spare oxygen tank and dived to within 3m of the seafloor before realising he hadn't turned the air on.
He resurfaced but did not dive down again and they returned to shore.
David Boldt, counsel assisting the coroner, questioned why it took the skipper nearly an hour before ringing 111.
"There's a lot of emotions going on in my head. I was peed off for a lot of reasons and I'm not going to tell why and I was just trying to think things over," the witness told police.
Asked why he didn't dive again to look for Thongsi, the skipper said that after four minutes without any bubbles, he thought she was dead. The boat would've also drifted away from the spot she was last seen, he said.
"I was just hoping that she would come up," the man said.
"I'm guilty for not going down the second time, if that's what you're saying. I should've gone back down."
On the shore, the skipper allegedly told a volunteer fisheries officer that he'd lost someone from his dive party, and that she had "sunk like a stone".
"I might have over-exaggerated. I can't remember saying it. You can't sink like a stone. You sink, like, naturally," he told the inquest today.
The fisheries officer will also give evidence, Boldt said, that "nothing felt right" about the way the skipper and his mates were reacting about losing a diver.
When asked about that today, the skipper said: "No comment."
The occupants of the boat were like "stunned mullets", he said.
"We were devastated."
Asked by Windley if he'd have done anything different that day, the skipper said he would've phoned emergency services immediately.
Thongsi's body was found just 100m from her last known position at a depth of about 10m.
Police National Dive Squad officers found nothing wrong with Thongsi's equipment, the inquest heard.
When she was found on the seafloor, she had nearly a full tank of air. Her gear functioned perfectly on a reconstruction dive.
A medical expert also found nothing in Thongsi's medical history to explain the sudden death of a seemingly healthy woman.
The inquest resumes on Friday.
