In my case the msi file was missing on my machine but your suggestion led me to another solution. The dowload of the current evernote (6.4.2) puts an msi file for the new version in c:\users\<your folder>\AppData\Local\Temp
If you browse to that location directly you can right click on the Evernote.msi file and click "Install" which allowed the Evernote install to complete without trying to update.
.MSI files typically have command line switches as well which you could use to force the update but I didn't need to use them in this case.
Also Note: In order to see the .msi files in the aforementioned directory you'll need to make sure your Operating System (mine is windows 7) has "Show Hidden Files and Directors" enabled.