Estimated project costs have tripled, corridor counties have defected and key proponents were politically ousted. Yet, the proposed $1 billion passenger-rail line from Minneapolis to Duluth remains on track for federal funding that could cover 80 percent of the project’s expenses, according to the Minnesota Department of Transportation.

The high-speed Northern Lights Express (NLX) has often stalled through seven years of planning and negotiations and has been overshadowed in the Twin Cities by light rail and the Northstar commuter line. But it has moved ahead into a $9 million preliminary engineering process that would make the project eligible for a federal grant by February 2016. New studies projecting ridership, expenses and the feasibility of the 150-mile line will be completed this summer, said MnDOT’s Frank Loetterle, the project manager.

“It’s a lofty goal of having a shovel-ready project in 2016, but we’re putting ourselves in the position of going after dollars at the federal level,” said Steve Raukar, the St. Louis County commissioner who chairs the NLX Passenger Rail Alliance.

But an alliance that already has seen the project’s estimated costs rise from $360 million in 2008 to the current $1 billion range and the withdrawal of two dues-paying counties — Anoka and Pine — has learned how quickly plans can unravel.

MnDOT surveys indicate support for this and other rail lines, but politics likely will determine whether a route that hasn’t been used for passenger rail in 30 years can be revived. By the time the last Amtrak passenger trains ran between the Twin Cities and Duluth in 1985, the trip took four hours, trains were often late, public subsidies were draining and ridership was falling.

While the Obama administration has supported rail projects, with Vice President Joe Biden an avid cheerleader who has urged the extension of the Northstar commuter-rail line to St. Cloud, elections this fall and in 2016 offer more uncertainty than guarantees.

The NLX line already has taken two huge political hits: The first came when the recently deceased Jim Oberstar, chairman of the House Transportation Committee and a big NLX backer, lost his congressional seat in the 2010 election.

Two years later, Dan Erhart, one of the line’s driving forces from the beginning, was defeated in his bid for re-election to the Anoka County board.

Before Erhart’s term had ended, the fiscally conservative Anoka County board withdrew from the NLX alliance. That departure saved Anoka County about $20,000 in annual dues while quietly infuriating other counties along the line. Anoka County has much to gain from NLX, with a proposed station at Foley Boulevard in Coon Rapids, considered a possible rail hub for the north-metro area and a link to the Northstar line.

Pine County’s withdrawal will save that county $5,250 in dues in 2015. That move has puzzled some, because Grand Casino in Hinckley is considered one of the line’s likely stops. The Mille Lacs Band of Ojibwe, an NLX Alliance partner, wants to realign track, bringing the train to the casino.

Raukar remains hopeful that Pine County will again come on board, but is less optimistic about Anoka County.

“We’re still confident we’ll move forward,” said Dan Krom, director of MnDOT’s passenger-rail office. “There’s a change and perception in public transit. There’s momentum here.”

Still to be determined are the location of stations, the number of round-trip routes per day — eight have been proposed — and ticket prices.

“Our objective is to pay for the operating costs out of fares,” Loetterle said.

“We don’t know if there is going to be [federal] money available to build in 2016,” Loetterle said. “But the climate for funding has changed. When the money falls from the sky, we need to be ready.”