In order to troubleshoot this issue, we first need to know which version of Revit you have installed and what is the current build number. The answer to both of these questions can be found in the About dialog. The header of the About dialog will display the name of the Revit version you have installed (About Autodesk Revit 2016, About Autodesk Revit Architecture 2016, etc.) and the build number is listed in the upper right corner (16.0.428.0 is the RTS version, 16.0.460.0 is SP1 and 16.0.490.0 is SP2).
Once we now the exact version installed, we can check if the downloaded R2 EXE file is appropriate. To do so, navigate to the C:\Users\<USER_NAME>\Documents\Autodesk Application Manager\{UUID} folder and check the name of the downloaded R2 EXE. For example, the R2 EXE file for Revit 2016 is Autodesk_Revit_2016-x64_R2.exe while the Autodesk_Revit_Architecture_2016-x64_R2.exe is for Revit Architecture 2016.
Tony Michniewicz
Autodesk Revit QA
Tony Michniewicz
Revit Software QA Analyst