It is recommend that you only use your backed-up Wowza Media Server configuration files as a reference to help you re-create your streaming applications in Wowza Streaming Engine Manager. Updated features may not work properly using Application.xml files from your Wowza Media Server installation and new features can't be configured. The Wowza Streaming Engine Manager user interface may not display Wowza Media Server configuration settings and/or unexpected behavior may occur.
You can still configure these applications in Wowza 4, but using applications from Wowza 3.5.x may not work with Wowza 4.0.x. You can configure them through the engine manager, or via .xml file configuration as per the previous versions of Wowza.