In 2001, the Harrisburg Heat picked up Knowles in the dispersal draft. That year, the NPSL disbanded and the surviving NPSL franchises created a new league, the Major Indoor Soccer League (MISL). At some time in 2002, Knowles moved from the Heat to the Kansas City Comets. On October 2, 2002, the Comets traded Knowles to the Philadelphia KiXX in exchange for Matt Caution. However, Knowles again experienced a considerable number of injuries and spent most of the season on the injured-reserved list.