In 2008, Union Station developers, Union Station Investco (USI), proposed new retail plans that would alter the historic Main Hall. As a historic building owned by the federal government and listed in the National Register of Historic Places in 1969, there is a federal requirement by the National Historic Preservation Act of 1966 that a Section 106 consultation must be carried out prior to any alterations. Originally, the marketing plans proposed two oblong openings on each side in the Main Hall floor just north of where the Center Cafe was positioned. The openings, equipped with up and down escalators, would allow patrons to access new retail in the lower level area that previously housed the movie theaters (which closed in 2009). The proposed plans presented in 2010, and revised in 2011, were determined to have an adverse effect by the Federal Railroad Administration (FRA) in June of 2012. In September of 2012, the proposed plans were modified to reflect feedback from consulting parties and to reduce the noted adverse effects.

In spring, 2016, after several years of discussion and plans, the FRA and State Historic Preservation Office (SHPO) concurred with a Memorandum of Agreement (MOA) resulting in the elimination of the Center Cafe and fountains in the Main Hall. The Center Cafe closed on March 1, 2016 and demolition on the restaurant space and fountains followed, with the Main Hall restoration completed in May 2016. To assist passengers, new directory boards displaying rail arrival and departure information will be installed in the transoms above the doorways leading to the train concourse, similar to their historic placement. New digital directories will be placed at entry points throughout the station, and digital signage will be installed in several locations in the Main Hall and retail concourse.