Create a new schema, with a new namespace. Call this “version 2”. If you choose to support version 1 XSD and version 2 XSD in your application that’s fine, but keep them seperate and don’t try to layer the two on top of each other – especially if you’re going try to stop people from using the version 1.
This is worth looking at as it describes some of what you’re dealing with:
archive of http://www.pluralsight.com/community/blogs/tewald/archive/2006/04/19/22111.aspx
I realise, however, that doesn’t really address your question. With regard to “is there a way to do this?” the answer is “no – not in a universally supported manner”. I’ve seen people add their own doc annotations to give hints, but this isn’t going to be universally understood by tooling.
Your best bet in the long run is to create come up with a versioning story for your schema(s) and keep version 2 seperate from version 1.