Well, if you're asking about nuts and bolts of HOW to do it, I did something similar making a script to convert from inline to standoff. I just had a template that matched the <choice>, selected the preferred child element (determined with a <choose> in the XSLT) and wrote it in that place, then wrote the remaining element into standoff with the appropriate target. I'm sure you could use something similar here, but using <note> instead of moving it off to standoff.
If you are asking whether this is a standard practice... I got nothing.