In the spring of 2009, when I began researching what would become a book about online community journalism, I couldn’t have found a better foil than the New Haven Register.

Owned by the bankrupt Journal Register Co. (JRC), the daily was moribund and mediocre, its disconnect from the community symbolized by its location: a gigantic converted shirt factory, partly surrounded by barbed wire, on the outskirts of the city next to Interstate 95. The contrast with the New Haven Independent, a nonprofit, online-only startup that is the focus of my book, couldn’t have been more stark.

Three years later, when I turned in my manuscript, things had changed considerably. JRC was out of bankruptcy. Its chief executive, John Paton, was winning industry plaudits for his “Digital First” strategy of accelerating the transformation from print to online. The New Haven Register had a new, young, progressive editor, Matt DeRienzo. And DeRienzo had outsourced printing to the Hartford Courant and had begun preparing to move his staff to a yet-to-be-determined location in the downtown. New Haven, a poor, largely minority city of about 130,000 people, was suddenly home to two of the country’s most closely watched experiments in reinventing local journalism.

So I was shocked on Wednesday when Jim Romenesko reported that JRC was once again entering bankruptcy. As Paton explained it on his blog, the idea is to get the company out from under the legacy costs that it took on when the newspaper business was a lot larger and more profitable than it is today: debt; long-term leases on buildings it no longer needs; and pension obligations. The strategy is to take advantage of Chapter 11 in order to reduce JRC’s cost structure and re-emerge from bankruptcy in a matter of months.

The pension piece has been the subject of considerable consternation on Twitter and elsewhere, as it raised the specter of out-of-state investors (JRC is headquartered in suburban Philadelphia) taking away from loyal employees what is rightfully theirs. DeRienzo countered by pointing out that pensions are guaranteed by the federal government. “No one’s retirement is at risk,” he wrote.

There’s no question that guaranteed pensions are largely a thing of the past in the private sector, with defined benefits having given way some years ago to the era of the 401(k). And JRC is not the only newspaper company with pension problems. In 2009, The New York Times Co. nearly reached a deal to sell The Boston Globe that would reportedly have brought in less cash ($35 million) than the Globe’s future pension obligations ($59 million), which prospective buyers were asked to assume.

In other words, if you were going to start any private enterprise from scratch, you would almost certainly not include pensions as one of the benefits that you would offer your employees. And I have little trouble believing that JRC’s pension system is weighing the company down.

On the other hand, it seems to me that JRC may soon face a “Where’s the beef?” moment. Paton’s tireless advocacy of Digital First has gotten a lot of attention and praise — deservedly so. At some point, though, Paton has to deliver real improvements both to the journalism of JRC’s news organizations and to the bottom line.

I think Paton and DeRienzo have the right values and the right motives. I’m rooting for them. Fundamentally, though, we are talking about trying to effect change from the top down. Corporate chain ownership has been a disaster for community journalism. I’d rather my paper be owned by a good chain than a bad one. But neither is an adequate substitute for local ownership — and yes, I realize that’s no panacea, either.

As the Lab’s Joshua Benton points out, this may be Paton’s last, best chance to remake JRC exactly along the lines that he envisions — truly a new start without the dead weight of his predecessors’ poor decisions dragging him down. I’m eager to see what he’ll do with that opportunity.