I have had to make updates to my app that I've submitted for Apple approval. I used the Xcode process to upload my original application to Apple. For the update, I just exported another Xcode set.
In order to retain all the existing information that was updated within Xcode with the prior release, I just replaced the files within the resources/www/project folder with the new files from the export.
This appears to have worked, although I'm not sure if I introduced some problems as certain functions behave strangely within the Xcode simulation environment.