Instead of overwriting the default configurations files supplied with the hugo-academic theme in the folder themes/hugo-academic/ , e.g themes/hugo-academic/assets/scss/bootstrap_variables.scss or themes/hugo-academic/assets/scss/main.scss these should be placed under the same name in the root folder assets/scss instead.
Hugo always prioritizes content in the root directory compared to themes/hugo-academic and in addition content in this folder will be overwritten in case that the theme is updated in the future....