Hi @Austin Barber ,
Web Servers and Application Servers are different web applications. Web Servers service the presentation layer and Application Servers perform processing. Therefore the files are different between the two. There are many that overlap between the two (i.e. the Core files), but there are many which are only applicable to the respect web application.
Based on the screenshot above, AppServer64 is an Application Server and Login is a Web Server. As @Roger Linhart mentioned, you would have to use the installer (Setup.exe) to upgrade a base instance of the Web Server and Application Server on this machine to EP5. Then from there, you could use WAMCON or manually copy the folder (and update IIS where applicable) to create a new web application for a different purpose (e.g. a second instance of AppNet or a second instance of AppServer).
I would hesitate on recommending you copy over a previous directory from a previous version of the web app (i.e. don't copy your OnBase Foundation EP5 files over an OnBase 18 web app). While it is possible all of the files will be overwritten, there is no guarantee and then you might have files from a previous installation in the new folder which could cause problems. Also, I would always assume the web.configs are different between versions (better yet, always assume web.configs are different even between builds) as there might be new settings or other changes. Instead, you should remove the previous configurations for the manually created web apps and then create a new ones either using WAMCON or manually (i.e. outside of the base installation which uses the installer and will be upgraded using the installer). Make sure to backup your web.config and note any other special configuration settings.
There is a section in the Web Server and Application Server MRGs about manual installation.
Best wishes.
