Flux returned to London in 1908 to take up a post as advisor to the Commercial, Labour and Statistics Department. In 1918, he was appointed Head of the Statistics Department of the Board of Trade. The Royal Statistical Society awarded him the Guy Medal in Silver in 1921 and in Gold in 1930. He also served as President of the Society between 1928 and 1930.
Flux retired to Denmark in 1932 and was knighted in 1934. He died of pneumonia in 1942, aged 75.