Reply To: Maintaining footnotes on import

First, make sure that “all information” is checked in the preference panel, before importing.
Next, create a char style, named “superscript” (or whatever), and just fill in “superscript” (no font name, nothing, just superscript).
Import the text and before doing anything else, run the find and change (text tab) to replace everything in superscript (find field empty, but in the find box below check “superscript) with the char style “superscript” (replace field empty, but in the box below select the char style for the superscript). Afterwards you can apply any style you want, the superscripts will stay.