The Reagan administration is on its way out, and with it goes the protection for the president's pet project, the Strategic Defense Initiative (SDI). Defense Department bureaucrats are biting their nails, and SDI is not their only concern.

Our sources say that any program that might look like a cousin to SDI could also be in danger if Congress decides to wipe out any vestiges of SDI. Military strategists are calling it "the leprosy effect"; anything that has touched SDI is in danger of being tainted.

The Air Force is so worried that it has moved about $1 billion in strategic programs out from under the SDI umbrella. It is a paper shuffle that may not work, even though most of the programs were begun before President Reagan launched the SDI research in 1983.

Congress has already ordered an investigation of one program that for a time was bundled up with SDI research. It is the boost surveillance and tracking system (BSTS), an early-warning space sensor originally designed to detect the launch of Soviet missiles. It also can be used to guide U.S. missiles to bring down Soviet weapons, and that gives it an SDI connection. Congress is worried that BSTS might violate the 1972 Antiballistic Missile (ABM) Treaty.

As we have reported, Reagan has danced around the ABM Treaty when it comes to SDI. The treaty implies that if research on space-based weapons goes ahead, the Soviets and Americans must sit down for renegotiations.

In 1985, Reagan signed a secret national security directive that said the administration had found new ways to interpret the ABM Treaty, but that as long as Congress went along with funding for SDI, there would be no need for any creative interpretation.

With Reagan's second term ending next January, Congress may feel free to use the ABM Treaty to whittle away at bits and pieces of SDI, on the grounds that they violate the agreement.

The investigation of BSTS ordered by Congress is seen by some in the Air Force as the first step toward canceling the program because of its possible conflicts with the ABM Treaty. Many lawmakers see BSTS as a wolf in sheep's clothing, an SDI program disguised as an early-warning system.

The report for Congress on BSTS is due within in a couple of weeks.

In the meantime, the Air Force is moving ahead with BSTS in spite of what the future may bring. Grumman Space Systems and Lockheed Missile and Space Co. are 11 months into a competitive ground-demonstration program. Their research is supposed to take 34 months and cost $304 million.

The Air Force has a second program that also could feel the hot breath of Congress because of the taint of SDI. That is the space surveillance and tracking system (SSTS).

While BSTS keeps track of Soviet missiles in the booster phase, SSTS is designed to track the missiles after they are lifted into space. That smacks loudly of SDI, but even SSTS has a non-SDI function: general surveillance of space.