The bankruptcy of commercial mortgage giant Capmark Financial underscored the continued deterioration of commercial markets nationally, but it may lead to some interesting maneuvering locally.

Capmark, the former commercial mortgage arm of GMAC, filed for Chapter 11 bankruptcy protection Sunday afternoon, after racking up $2.3 billion in losses through the first six months of 2009. It had been warning of liquidity problems for several months.

Capmark is the lender on Seaport Square, the $3 billion project proposed by Gale International and bankrolled by Morgan Stanley. In 2006, Capmark provided a $155 million mortgage on Gale and Morgan Stanley’s $204 million acquisition of 23 vacant acres along the South Boston waterfront.

Now, industry insiders are speculating that Morgan Stanley may use Capmark’s bankruptcy to buy the Seaport Square note at a discount. Such a move could allow Morgan Stanley to substantially reduce its carrying costs while essentially paying itself to hold the South Boston properties.

Gale CEO John Hynes has repeatedly described Seaport Square as a long-term play. Gale and Morgan Stanley envision eventually building out 6.5 million square feet at the waterfront.

Morgan’s ability to swipe the Seaport Square mortgage at a discount will depend on how Capmark’s Delaware-based bankruptcy court judge treats the commercial lender’s assets – whether he allows the bankrupt lender to sell individual loans piecemeal, or cuts them up into regional tranches, or sells them as a single offering. The latter two scenarios wouldn’t favor a move by Morgan Stanley, which has been stung recently by its commercial real estate holdings.

In its bankruptcy filing, Capmark listed assets of $20.1 billion, including a $10.7 billion loan pool, and liabilities of $21 billion.