Complex sentence: It was not until the 21st century that they started occupying historic flagship stores throughout the country, however they have yet to close the downsized downtown flagship locations of former chains Jordan Marsh in Boston, Wanamaker's in Philadelphia and Marshall Field's in Chicago.
Split into simpler sentences: It was not until the 21st century that they started occupying historic flagship stores throughout the country. However they have yet to close the downsized former downtown flagship locations of chains Jordan Marsh in Boston, Wanamaker's in Philadelphia and Marshall Field's in Chicago.