How can i apply a CharStyle for created footnote on the fly? [CS6-jsx]

also you are overcomplicating things a bit by first storing the footnote text in a temp variable, removing the content of the found text (error proned, might invalidate the insertion point reference).

here is a function from a larger script of mine (also handles somewhat footnotes in tables):

  function dofn(sel) {
    var pare = sel.parent.getElements()[0];
    var ip = sel.insertionPoints[0].index;
    //Special case for fn in tabel
    if (pare instanceof Cell) {
      var fake = pare.texts[0].insertionPoints[ip].contents = (app.activeDocument.footnoteOptions.showPrefixSuffix == FootnotePrefixSuffix.PREFIX_SUFFIX_BOTH || app.activeDocument.footnoteOptions.showPrefixSuffix == FootnotePrefixSuffix.PREFIX_SUFFIX_REFERENCE) ? app.activeDocument.footnoteOptions.prefix + 'XX' + app.activeDocument.footnoteOptions.suffix : 'NN';
      pare.insertionPoints.itemByRange(ip, ip + fake.length).getElements()[0].appliedCharacterStyle = app.activeDocument.footnoteOptions.footnoteMarkerStyle;
      ip = pare.parentRow.parent.storyOffset.index + 1;
      pare = sel.parentStory;
   //   errors.push("Footnote found in table; Reference moved at the end of table");
    }
    var fn = pare.footnotes.add(LocationOptions.BEFORE, pare.insertionPoints[ip]);
    sel.move(LocationOptions.BEFORE, fn.texts[0].insertionPoints[-1]);
    fn.texts.everyItem().applyParagraphStyle(app.activeDocument.footnoteOptions.footnoteTextStyle)
    return fn
  }