I have a singe webrole in my azure account and I want to mantain 2 webapps on it. I have deployed them. Now one of the sites got an update and I want to deploy only this one. I'm using cspack to create packages cause I'm customizing some files after the publishing.
I don't believe this is possible; the upgrade package requires the complete configuration for both sites.
In any case, why would you only want to update one of the applications? Given that you have at least two instances to provide failover during deployment you should see no down-time, just higher application load.