It's been nearly four years since Kraft and Heinz merged — a deal applauded by some on Wall Street as the chance for private equity firm 3G Capital to exercise its reputation for cost-cutting and dealmaking.

The results have been disappointing and raise the question of whether 3G's model really works. The firm, which has roots in Brazil and made much of its initial money in railroads, has had to run a packaged food company just as the industry turned on its side.

Kraft Heinz late Thursday handed investors a raft of bad news that only added to the string of disappointments from the ketchup maker. It revealed it received a subpoena from the Securities and Exchange Commission in October related to its accounting policies and internal controls. It delivered earnings and revenue that were sharply lower than estimates, slashed its dividend by 36 percent and took a $15 billion write-down on two of its biggest brands, Kraft and Oscar Mayer.

"We believe these impairments validate fears that Kraft Heinz may have been more focused on costs than building brand equity, and even if management now has 'seen the light', we are now concerned that its brands lack the equity to drive pricing power needed to compete and drive growth in a sustainable way," said Piper Jaffray analyst Michael Lavery.

On Friday, shares cratered more than 28 percent to a 52-week-low, lopping off more than $16 billion in market value from the stock.

Kraft Heinz attributed its miss to operational challenges. The company said it stands by its famed zero-based budgeting approach to cost-cutting, in which managers need to justify all costs. It faced pressure from supplier negotiations, delayed manufacturing projects and rising costs.

"We are overly optimistic on delivering savings that did not materialize by year-end," said CEO Bernardo Hees, a 3G Capital partner. "For that, we take full responsibility."

Those setbacks came amid tastes that have changed away from packaged food like Oscar Mayer deli meat and Capri Sun drink pouches toward upstart brands with healthier images created by smaller companies like Kind Bar.

But analysts and investors have wondered whether there is a deeper problem with 3G's approach. Its model, in large part, depends on dealmaking: 3G buys a slow-growing company like Kraft, slashes excess costs and then moves on to another acquisition. It's the same approach that 3G has applied to the beer industry with Anheuser Busch Inbev. But Kraft Heinz hasn't done a deal in years, far longer than most investors expected.

Kraft Heinz was publicly and embarrassingly rebuffed by Unilever in 2017 — a rejection that some say emboldened other food companies, which once feared Kraft Heinz, to realize they too could say no to the company and its 3G backers. As Kraft Heinz's shares since have fallen roughly 60 percent, a potential deal has become even more challenging, particularly because one of its biggest backers, Warren Buffett, is opposed to hostile takeovers

Already, at least two potential deals have slipped by. Kraft Heinz passed on the chance to acquire Pinnacle Foods, CNBC previously reported. When Campbell Soup was forced to evaluate a sale under activist pressure last year, Kraft Heinz did not step up with any meaningful premium to buy the soup company.

Without a deal, Kraft Heinz has had to navigate the challenging prospect of managing a big food company just as tastes are moving markedly away from them.