Prior to cutting the text, I use the Clear All Formatting tool (it's on the Home Tab in the Font Group) to strip out everything from the source text. This gives me a clean block of text to paste into the new document. Unfortunately, this also clears out superscripts and subscripts. After pasting the text, I compare the two documents and retag the appropriate text (CO2 becomes CO2, for example).
But, when it comes time to proof, I need to go through the entire source document and search for all instances where the author used a subscript or a superscript. In a long document after a busy day, I can't rely on my eyes to catch each and every tiny number or letter. So, I found this process at this site, and it allows MS Word to find and highlight all instances of subscript (and a second pass finds the superscripts) using the standard Find/Replace tool in MS Word.
Thanks to Allen Wyatt for posting this great MS Word Tip:
Since it's his material, I'm not going to reprint it here without permission. Just follow the link and thank him for this ingeniously simple, but useful, power user tip.