This sudden and drastic change in the operations at Lincoln posed a direct threat to the continued preservation of the Old Courthouse Museum and the rest of the Lincoln State Monument. When the Museum of New Mexico resumed control of the properties in 1979, it did so with absolutely no legislative budget for operations. During the 1980 legislative session, the Museum of New Mexico requested a $98,100 annual budget for the Lincoln State Monument.  Although partially funded, State Monuments Director Thomas Caperton continued to appeal to the Museum of New Mexico Board of Regents for additional money, specifically for more staff and much-needed maintenance work in Lincoln—especially for the courthouse.  With limited funding, the State Monument Staff worked to address issues at the site, including the Old Courthouse Museum. In 1980, the staff closed the building to the public for several months to update the structure’s electrical wiring, which had recently failed. 

While the State of New Mexico debated the issue of funding and control over the Lincoln State Monument, the Lincoln County Heritage Trust continued to move forward with its mission. Led by Executive Director Johnny Meigs, the organization restored the historic Luna House in Lincoln and constructed a brand new building (now the Anderson-Freeman Visitor Center) for use as a purpose-built museum and headquarters. The two new attractions opened in June 1981, and Lincoln saw a noted spike in visitation. 

During the 1980s, staff members and volunteers from the Lincoln State Monument and Lincoln County Heritage Trust completed several major preservation projects in town. One of the most critical undertakings was the creation of a comprehensive Historic Structures Report for Lincoln's state-owned properties. This planning document was spearheaded by State Monuments Director Thomas Caperton and partly funded by the National Park Service and the New Mexico State Historic Preservation Office. The report included historical narratives for all of the structures, researched by local historian and Lincoln County Historical Society President Nora Henn, and architectural drawings detailing the construction methods of each building. The report, completed and published in 1983, provided a road map for future preservation efforts in Lincoln. 

While working on the Historic Structures Report, State Monument leadership turned to the state legislature for continued funding for Lincol’s cultural resources. In 1982, the state earmarked $346,000 from state-issued severance tax bonds to support a significant restoration project at the Old Courthouse Museum and other buildings in Lincoln.  Unfortunately, the state never sold the severance tax bonds due to a ruling from the Internal Revenue Service questioning their tax-exempt status. Monuments Director Thomas Caperton returned to the legislature the following year and successfully gained the appropriation again, which became available in July 1983. Finding a qualified architect, engineer, and contractor delayed the project even further, and restoration work on the courthouse and other buildings did not start until 1985. During the year-long project at the Courthouse, contractors stabilized the structure and removed the staff offices and bathrooms that the Old Lincoln County Memorial Commission added in the 1960s. The State Monument Division restored the historic Watson House in the middle of town to replace their offices during the Courthouse renovations. Under the leadership of Head Ranger Jack Rigney, the Lincoln State Monument staff worked closely with the Lincoln County Heritage Trust to provide visitors with a seamless interpretive experience. Executive Director Gary Miller and Bob Hart of the Heritage Trust signed agreements with the State of New Mexico to offer joint tickets for Lincoln's museums and historic structures. The two organizations also developed joint programming, built exhibits, and co-wrote several preservation grants throughout the 1980s and 1990s.   

In 1999, the Lincoln County Heritage Trust made the difficult decision to pass ownership and management of all of its properties in Lincoln to another non-profit organization, the Hubbard Museum of the American West. One of the final projects undertaken by the Lincoln County Heritage Trust was the organization’s enthusiastic support for the creation of a National Scenic Byway loop throughout Lincoln County. This dream came true in 1998 when the United States Department of Transportation officially designated an 83-mile loop through Lincoln County as the Billy the Kid National Scenic Byway. The nationally recognized and marketed byway cut directly through Lincoln and brought a renewed sense of optimism for the future of heritage tourism in the region and new potential funding sources for preservation projects in Lincoln and beyond.

Capitalizing on these new opportunities, the National Park Service awarded the  Hubbard Museum of the American West a Save America’s Treasures Gran for preservation work throughout historic Lincoln. The work, completed in 2003 and 2004, included significant restoration work on four buildings in Lincoln: the Luna House, the Gallegos House, the Dr. Wood’s Annex, the Dr. Wood’s House, and the ruins of the former Aragon Store and Ozanne Stage station. The Hubbard Museum’s investment in Lincoln brought new life to the old town, but the organization’s time there proved brief. In 2005, the State of New Mexico negotiated with the Hubbard Museum to accept donations of all their historic Lincoln properties. The Museum of New Mexico Board of Regents unanimously voted to receive the gift in September 2005 and took official ownership of the property in early 2006. 

After nearly 70 years of formal preservation work in Lincoln, the majority of the town's historic structures fell under the stewardship of the State of New Mexico. Since then, the Department of Cultural Affairs and New Mexico Historic Sites staff have engaged in dozens of significant preservation projects throughout the town and countless hours of routine maintenance. Today, Lincoln stands as one of the best-preserved historic towns in the American West, a testament to the tireless efforts of its citizens, civic leaders, and the professional staff of the many organizations that have worked to preserve its history.