Promoted to No 3 in the order, the Black Caps left-hander was eyeing up a maiden test century in the first test against the West Indies at the University Oval in Dunedin.
However, he was denied an opportunity to raise the milestone when he became the first New Zealand victim of the experimental law which allows players to appeal an umpiring decision.
On 95 he was struck on the bat by Windies skipper Chris Gayle, whose appeal for lbw was turned down by debutant umpire Amish Saheba.
The decision was reversed after Gayle requested the decision to be referred to third umpire Rudi Koertzen.
Flynn was naturally disappointed but philosophical about the decision.
"I thought I had [got outside the line] but once I've looked at it again, well, you can't really argue with it can you?"Waiting for the decision, which seemed to take an age, was a nerve-wracking experience.
"I initially thought I was OK . . . The West Indies boys were asking me how I was feeling. I was pretty calm to start with but once it started dragging out a bit longer, the nerves started creeping in."
Gayle's first instinct was that it was out and did not waste much time asking for the decision to be referred.
"I thought it was pretty close. I wouldn't be shouting if I thought it was missing," he said.
"I knew it was close when it was taking a while. But normally in those cases the batsmen get the benefit of the doubt. So I figured that was going to happen in this case."
Flynn was Gayle's third victim and he finished the day with three for 42 from 20 overs.
He was happy to pad out his figures with Flynn's wicket but also expressed some empathy for his opponent.
"You know, if I was the batsman, I'd be pretty disappointed. Flynn batted pretty well even though it was a good wicket to bat on. I thought he really assessed the conditions as quickly as possible. "It is just unfortunate he missed out on a 100."
Gayle said it was the first time he had played under the experimental rule and did not want to rush in to assess its merit.
However, so far the system had served him well.
"It is the first time using it and so far we've been successful," he joked.
