Thornburg Mortgage Inc. (TMA), the ultra-jumbo mortgage lender that has been staring at possible extinction on and off over the course of most of 2008, said in a filing with the Securities and Exchange Commission Tuesday that its survival is in doubt. Questions over the company’s future remain despite a last-ditch $1.35 billion financing plan that saved the company from bankruptcy in late March. In its filing, the company said that “recent adverse developments in the mortgage finance and credit markets has adversely affected our business, our liquidity and our stock price,” raising doubt over the company’s ability to continue as a going concern. Other warnings over the company’s available liquidity to service its existing debt may have come as a surprise to some investors, who generally believed the company to be in clear after the March investment led by private equity firm MatlinPatterson Global Advisers LLC. Like hundreds of other mortgage operations, the Santa Fe-based lender has been hit hard during the downturn — but what makes Thornburg’s predicament different is the company’s focus on high-balance, or ultra-jumbo, lending; the company also has not been plagued with credit quality concerns over the loans on its portfolio, with 60+ day delinquencies at just 0.65 percent of the company’s $23.5 billion loan portfolio at the end of March. Thornburg also said it had been subpoenaed by the SEC over its restatement of 2007 results, including “the valuation, impairment and/or disclosures concerning the accounting treatment for the company’s mortgage-backed securities addressed in the restatement.” One major hurdle yet remains for the lender, as well, in order for its so-called “Hail Mary” financing plan set into motion in March to work: 90 percent of existing preferred shareholders must agree to sell their shares for $5.00. While many shareholders are unhappy, given the $25.00 face value of the securities, they likely face little choice, sources told HW on Thursday morning. “It’s $5.00 or zero, pretty much,” said one shareholder that spoke with HW, asking not to be identified by name. Preferred shareholders have until June 30 to tender shares under the offer. Thornburg noted in its filing that success of the tender offer “is outside of our control.” Disclosure: The author held no positions in TMA when this story was originally published. HW reporters and writers follow a strict disclosure policy, the first in the mortgage trade.