After quite a bit of experimenting I have got it to work.
Open Find and replace - Replace In the Find what - open format (bottom left) - Choose Font and make sure that only superscript is ticked. Then in Replace with - open format - Choose font and untick all boxes making sure that none are still coloured (filled). Then use standard find and replace. You do not have to put any letters in the boxes as it should look for the format and replace.
Hope this works for you too.