As per your post, I think your work flow is entirely XML based. As far as I can see it is better to import entire XML, because updating only changed XML structure will leave a margin for errors. To avoid that very small window for margin of error will be killed if you update entire XML.
But there is one more point if you update entire XML, you might have to put some more scripting if anything is getting changed(like paragraph style or character style) for those you need to do something, but after that no exception you will meet.
You're right, My work flow is based on XML and i already have the functionality to update the entire XML with some scripting files. I can understand your suggestion but, our client requirement is to update only the modified xml contents in the InDesign documents without disturbing other contents. Is there is any way to do it?????