MSDeploy: "Leave extra files on destination" from command line?
For msdeploy.exe you need to add -enableRule:DoNotDeleteRule to ensure content is not deleted. For more info on MSDeploy rules see http://technet.microsoft.com/en-us/library/dd568992(WS.10).aspx.
If you want to choose which dirs need to be leaved, you can read http://blog.alanta.nl/2011/02/web-deploy-customizing-deployment.html