Flynn carved up his 10th first-class ton, 19th for ND and amassed 5000 runs in the format when just on 14 runs.
No 4 Bharat Popli eventually succumbed to debutant Liam Dudding for 172 runs, his third shield century.
The new ball will be due in 10 overs today for Flynn who will have the choice to pad up for a second dig or make the Stags bat again.
No doubt, No 9 Ajaz Patel and No 11 Dudding have the arduous task of taking that option away from Flynn if they go on to forge a 50-run partnership but Young, while mindful that anything can happen, was circumspect.
"It's not their job. It's the job of the top six or seven batsmen to post a substantial first-innings score," he said.
"Ajaz and Liam can battle on to take that decision out of ND's hand otherwise we'll just have to take it in our stride to play much better cricket tomorrow."
Should they shine the ball again, Young said it was imperative his bowlers put all six deliveries in the right areas and not two errant ones to release the pressure valve on the ND batsmen, as CD did in the Knights' first innings.
The batting strategy emphasised the need for the top six to face 250 balls to address what appeared to be a lack of mental application from the predominantly young players.
Manawatu's Mitch Renwick, in his third first-class game, is CD's top scorer with 69 at first drop.