Ryan,
See if this helps:
1.Stop all running instances of Web AppBuilder (Developer Edition) if any.
a. make sure you do not have any command prompt widows open. i.e named "Web AppBuilder for ArcGIS"
2.Open the Command Prompt window.
a.Click windows start button > All Programs > Accessories > Command Prompt !!! right click it and choose "Run as Administrator"
3.Browse to the \server directory of your newer version of the Web AppBuilder installation.
a. If you installed WAB Dev 2.0 on the C Drive (i.e. C:\web-appbuilder-2.0) then you need to type this into the command prompt window:
Type: cd\
Now press enter.
Type: cd\ web-appbuilder-2.0\server
Now press enter.
4. To upgrade all of your apps
a. If you installed WAB Dev 1.3 on the C Drive (i.e. C:\web-appbuilder-1.3)
b. Type: node upgrade C:\web-appbuilder-1.3