Boeing and the U.S. Missile Defense Agency are negotiating changes to the $3.5 billion contract to oversee the massive Ground-Based Midcourse Defense (GMD) missile shield system.

Boeing won the development and sustainment contract (DSC)—worth up to $10 billion over 10 years—over a Lockheed Martin/Raytheon team after a long battle. The work includes oversight of the missile defense system that protects the U.S. and its territories from ICBM attack. The forthcoming contract changes do not pertain to Defense Secretary Chuck Hagel’s March 15 decision to add 14 Ground Based Interceptors (GBIs) to the 30 already in silos at Fort Greely, Alaska, and Vandenberg AFB, Calif., says Roger Krone, president of Boeing Network and Space Systems.

At issue are “fact-of-life” changes in the GMD program since Boeing won the contract in late 2011. “There has been discovery. Things have happened. Things have changed,” Krone tells Aviation Week. “There is a need to realign DSC with the go-forward plan.” Krone did not provide details on the discoveries, and the Missile Defense Agency was unable to immediately provide details.

Krone, however, points out that Hagel has ordered a third flight test of GMD for this year. An intercept test of GMD using its legacy Raytheon Exoatmospheric Kill Vehicle is expected this summer. Though described as part of a routine program to ensure existing interceptors perform as planned, the test also will be a demonstration to North Korea that its promises to strike U.S. targets with nuclear-tipped ICBMs could be thwarted.

Already planned for 2013 were two tests of the GBI carrying an upgraded version of the EKV, called the CE-2. This system experienced guidance problems, contributing to the fact that GMD’s last successful intercept test was in December 2008. During a flyout test earlier this year, MDA already demonstrated that the EKV CE-2 functioned nominally with improvements. “We have to make sure we have a contract that now supports the program going forward,” Krone says.

Boeing shocked the competition in 2011 with its aggressive pricing when it won the DSC contract. Boeing’s bid was said to be 35% lower than the heritage DSC contract. The contract is a hybrid, containing fixed-price and cost-plus elements.