Hook is run, code is executed, but the tangled files have the original content

transpile.el

(defun svg2code/transpileES5 ()
  "Transpiles the current javascript-mode buffer from ES2015 to ES5"
  (when (and (string-match ".js$" (buffer-file-name))
             (not (string-match "exports.*" (buffer-file-name))))
    (shell-command-on-region
     (point-min) (point-max)
     "babel --no-babelrc --compact false --presets env"
     (current-buffer)
     t
     "*Babel Error Buffer*"
     t)))

(defun svg2code/run-before-save-hook ()
  (run-hooks 'before-save-hook)
  (save-buffer))
 
(add-hook 'js-mode-hook (lambda () (add-hook 'before-save-hook 'svg2code/transpileES5)))
(add-hook 'org-babel-post-tangle-hook 'svg2code/run-before-save-hook)

Updated with a working version