Even Back in the Day, the shortest rail connection from Sioux Falls to Brookings would have been north on the Great Northern to Arlington, then east on the C&NW to Brookings. The GN now only goes as far as Wentworth (and then hangs a left on the old Milwauke Road and ends in Madison). I believe is state owned and used by BNSF.
South Dakota always had a shortage of rails going north and south and now the only one left is Sioux City to Aberdeen.