By sheer luck, considering where the Cowboys eventually found their quarterback in that draft, they instead will travel to Denver with Prescott -- a winner in 14 of his first 17 regular-season starts, last year's Offensive Rookie of the Year and 2017 captain -- as their starter.
Lynch will be inactive for the Broncos because of a shoulder injury, but the injury aside, he has been unable to beat out Trevor Siemian for Denver's starting job the last two seasons.
"I do know this: When you're in a draft, there's a lot of conversations about a lot of players, at every position, with every pick -- moving up, moving back, and all of that," Cowboys coach Jason Garrett said. "We're obviously happy with the quarterback that we have."
It's easy now to say the Cowboys made the right decision, but after the first night of the 2016 draft, Jones couldn't sleep.
He went to bed at about 3 a.m. after selecting RB Ezekiel Elliott with the fourth overall pick. But he lamented the player who got away. After waking up three hours later, he started talking to colleagues around the league and was still upset.
In Elliott, the Cowboys had the running back who could succeed as DeMarco Murray had in 2014. But Jones saw Lynch as Tony Romo's future replacement.
When Lynch started to fall in the first round, the Cowboys called a number of teams that had selections later in the round. They did not find a willing trade partner until they got to the Seattle Seahawks, who owned the 26th pick.
The Cowboys offered Seattle their second- and fourth-round picks. They hoped picks Nos. 34 and 101 would be enough for Seattle to do the deal. But then the Broncos got involved and offered the Seahawks their first-round pick, No. 31 overall, and their third-rounder, No. 94, and moved into position to take Lynch.
Jones was reluctant to part with the Cowboys' third-round pick, No. 67 overall. They were coming off a 4-12 season and needed to fix the defense. At least that was the plan entering the draft.
Whether Seattle would have taken the 34th and 67th picks from the Cowboys over the offer from Denver is impossible to know, but Jones almost immediately wished he had upped the ante.
"I really have added it up," Jones said after the draft, "and you all don't need philosophy here, but ... when I look back on my life, I've overpaid for my big successes every time, and when I've tried to get a bargain or get a little cheaper or get a better deal on it, I ended up usually either getting it and not happy I got it or missing [it].
"I probably should have overpaid here."
"The potential is overwhelming," Garrett said of Lynch at the time.
About five weeks before the draft, Garrett, Jerry Jones and Stephen Jones left the owners meetings in Boca Raton, Florida, to see Lynch work out at Disney's Wide World of Sports in Orlando, where they were met by Will McClay, Lionel Vital and Chris Hall, three of the bigger voices in Dallas' draft room, and offensive coordinator Scott Linehan and quarterbacks coach Wade Wilson.
Of all the quarterbacks the Cowboys worked out that spring, Lynch was the only one Jerry Jones came to see.
Lynch had a good but not great workout. He started slowly. But once Linehan and Wilson began directing the session, Lynch got better and his passes showed zip. The Cowboys did not leave Orlando salivating so much that they thought they had to get Lynch, but they liked him.
It wasn't until Lynch was available midway through the first round that the Cowboys were intrigued. But then Jones pulled back, reluctant to go all-in for a quarterback the Cowboys believed could be Romo's heir.
This decision was made more puzzling because of 2014 draft.
As much as Jones lamented missing out on Lynch, he had lamented even more missing out on Johnny Manziel two years earlier. With the 14th overall pick, the Cowboys could have had Manziel, the Heisman Trophy-winning quarterback from Texas A&M. Jones loved everything about Manziel, from his game to his moxie to the marketing possibilities.
As the minutes ticked away before Dallas made its 2014 first-round pick, Jones brought up Manziel's name in the draft room and was met with silence. Instead, the Cowboys chose Zack Martin. All Martin has done is become one of the best guards in football. Manziel has been out of the league since 2015.
In the second round of that draft, the Cowboys made a bold move up from No. 47 overall to No. 34 in a trade with the NFC East rival Washington Redskins. They viewed DeMarcus Lawrence as the last pure right defensive end ready to make an impact as a rookie and gave up their second- and third-round picks to get him.
Two years later, however, Jones was reluctant to part with the same picks for a potential franchise quarterback.
Jones still ended up with Romo's heir in Prescott, although it required more than just missing out on the trade that would have landed Lynch.
The Broncos were interested in Prescott, who was Lynch's roommate at the scouting combine, and used one of their 30 pre-draft visits on him. They saw Brock Osweiler walk in free agency, signed Mark Sanchez, and had Trevor Siemian, but they wanted a potential developmental quarterback.
The Broncos decided to bring Prescott to Denver for a workout. But he missed his flight from Orlando.
"One of my first times flying out of there where I was training," Prescott said. "I guess it's the No. 1 place to fly out of -- didn't make it to the gate. The doors shut."
He eventually made it to Denver but knew being late was not good.
"I'm sure the quarterback not making the flight doesn't help," Prescott said.
Prescott didn't miss his flight to Dallas for a pre-draft meeting, but the Cowboys nonetheless waited until the fourth round to take him. He wasn't even their first fourth-round pick. That was Charles Tapper. Prescott was the 135th pick overall.
Missing out on Lynch might be the best move Jerry Jones has made.
"Everything," Prescott said, "happens for a reason."