As long as the actual footnote is displayed correctly, you should be able to update the cross-reference that points to the footnote. Select the cross-reference and use F9 or Fn+F9 depending on your keyboard.
If this fails to work, ensure that the reference is still an "active" cross-reference field. Press Alt+F9 (or Alt+Fn+F9) to reveal field codes and report back what you see in place of the cross-reference.