See http://blogs.msdn.com/b/kwill/archive/2012/10/05/windows-azure-disk-partition-preservation.aspx for information about what is preserved on an Azure PaaS VM in different scenarios.
In short, the only things that will truly persist are things packaged in your cscfg/cspkg (ie. startup tasks). Anything else done at runtime or via RDP will eventually be removed.