In the Devils Highway, why did Maradona abandon Mendez and the group last minute? Was he himself afraid of the route change they had to do, or did someone tell him to leave?

Those are great questions! In The Devil’s Highway, Maradona is supposed to be the “old pro,” the one who knows exactly how to lead walkers into the United States and turn them into cash. He was ready to make the journey. So why did he abandon the travelers?
Basically, the story never directly answers these questions for us, but our best guess is that Maradona was afraid of the route change, fearful that it would be unsafe, that he couldn’t find his way through it, or perhaps even that he would get caught.
Let’s take a look at the evidence.
We know from Chapter 3, “The Coyote and the Chicken,” that Maradona is being controlled by the gang.
And from Chapter 5, “Jesus Walks Among Us,” we know that the gang sent Maradona and Jesus on a new route that made them nervous:

So Jesús and Maradona were sent to Sonoita. Hey, what the hell. It didn’t make no nevermind to them: they’d been in San Luis a long time, and they’d used it up… They only had one real concern. They were going to new desert, to the center of the Devil’s Highway. But El Negro had a couple of locals ready to show them the ropes. Nothing to worry about.

From Chapter 6, “In Sonoita,” we know that Maradona is the type of person to duck and run if trouble arises, leaving everyone else to fend for themselves:

They got past town, and hours later they arrived at a water tank beside a paved roadway. This nameless outpost was the El Negro gang’s chosen rendezvous. There, the group rested and drank as they waited for the pickup. But instead of their own driver appearing, a Border Patrol truck found them. Maradona managed to escape with one pollo, running into the scrub. The two men went on to Phoenix. Mendez and his group of twelve were apprehended.

Finally, it’s in Chapter 7, “A Pepsi for the Apocalypse,” that Mendez realizes how Maradona has abandoned the group, never to be seen again:

But Maradona’s apparently gone. Either that, or he’s so drunk Mendez can’t wake him. … Mendez will always wonder what happened to his homeboy.

Look closely at how El Negro reacts to the news that Maradona has abandoned the group:

"All right", El Negro says. "I’ll handle it. I’ll call Santos and Lauro."

Does it sound to you like the boss, El Negro, had secretly told Maradona to leave, that he's just keeping this information from Mendez? It doesn’t sound that way to me, especially considering how El Negro then had to pay two people to do Maradona’s job.
So, as a reader, I take my best guess: Maradona was probably afraid of the unknown route, and that’s probably why he abandoned the group.