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Allen was on his final flying lap in the 20-minute session when his Holden ZB Commodore cranked sideways on approach to Reid Park.
The Eggleston Motorsport driver tried to recover from the slide but slammed into the outside wall and ground to a halt on approach to McPhillamy Park.
That brought out the red flag and ended the session with less than a minute remaining.
Eggleston Motorsport is in a race against the clock to assess the damage and determine whether the car can be fixed in time for Race 9 on Friday afternoon.
Allen was set to drive the #17 Dick Johnson Racing Ford Mustang in Practice 3 with Will Davison but the team elected to have him sit the session out.
Boost Mobile Qualifying ends in CHAOS!!!
Kai Allen finds the wall HARD and triggers a red flag! #Super2 #Super3 pic.twitter.com/UZaGmUp7Wj
— Dunlop Series (@Dunlop_Series) October 10, 2024
All told, it was Brad Vaughan who blitzed the session with a time six tenths quicker than his nearest rival Jobe Stewart for Image Racing.
The Tickford Autosport driver nearly eclipsed the lap record set by Zak Best a year ago, Vaughan topping Friday morning’s session on a 2:04.7537s.
Vaughan, who is on double duties in the Matt Chahda Motorsport Chevrolet Camaro wildcard, was the only driver to dip under the 2:05s bracket.
Allen lost his fastest lap time as a result of bringing out the red flag, pushing him down to 15th in the session.
His nearest title rival Zach Bates was only 13th in the session after he suffered a puncture on his last flying lap. Allen leads the Super2 Series on 1032 points while Bates has 906 points to his name.
Behind Vaughan and Stewart came Rylan Gray (Tickford Autosport) and his teammate Lochie Dalton.
Aaron Cameron, who had been fastest early in the session, was fifth for Kelly Racing. The top 10 was completed by Max Vidau, Jarrod Hughes, Jordyn Sinni, Campbell Logan, and Reuben Goodall.
Race 9 of the Dunlop Series is scheduled for 3:20pm AEDT on Friday. That session precedes qualifying for the Repco Supercars Championship at 4:15pm AEDT.
Results: Dunlop Series Bathurst 1000, Qualifying
| Pos | Num | Driver | Team/Sponsor | Car | Lap | Diff |
| 1 | 5 | Brad Vaughan | Tickford Racing | Ford Mustang GT | 2:04.7537 | |
| 2 | 99 | Jobe Stewart | Erebus Academy | Holden ZB Commodore | 2:05.3761 | 0.6224 |
| 3 | 55 | Rylan Gray | Tickford Racing | Ford Mustang GT | 2:05.4128 | 0.6591 |
| 4 | 5 | Lochie Dalton | Fiducian Racing | Ford Mustang GT | 2:05.5209 | 0.7672 |
| 5 | 27 | Aaron Cameron | SCHRAMM Group Racing | Ford Mustang GT | 2:05.6845 | 0.9308 |
| 6 | 17 | Max Vidau | Anderson Motorsport | Ford Mustang GT | 2:05.9278 | 1.1741 |
| 7 | 118 | Jarrod Hughes | Image Racing | Holden ZB Commodore | 2:05.9343 | 1.1806 |
| 8 | 54 | Jordyn Sinni | Eggleston Motorsport | Holden ZB Commodore | 2:05.9855 | 1.2318 |
| 9 | 2 | Campbell Logan | Walkinshaw Andretti United | Holden ZB Commodore | 2:06.0543 | 1.3006 |
| 10 | 20 | Reuben Goodall | Gomersall Motorsport | Holden ZB Commodore | 2:06.4726 | 1.7189 |
| 11 | 88 | Jonathon Webb | Eggleston Motorsport | Holden ZB Commodore | 2:06.5572 | 1.8035 |
| 12 | 3 | Thomas Maxwell | MW Motorsport | Nissan L33 Altima | 2:06.5876 | 1.8339 |
| 13 | 25 | Zach Bates | Walkinshaw Andretti United | Holden ZB Commodore | 2:06.6578 | 1.9041 |
| 14 | 9 | Cody Gillis | Brad Jones Racing | Holden ZB Commodore | 2:07.1185 | 2.3648 |
| 15 | 1 | Kai Allen | Eggleston Motorsport | Holden ZB Commodore | 2:07.3993 | 2.6456 |
| 16 | 15 | Cody Burcher | MW Motorsport | Nissan L33 Altima | 2:07.6332 | 2.8795 |
| 17 | 19 | Elliott Cleary | Brad Jones Racing | Holden ZB Commodore | 2:08.1527 | 3.3990 |
| 18 | 37 | Jackson Rice | Matt Chahda Motorsport | Holden ZB Commodore | 2:10.0295 | 5.2758 |
