I had a similar issue. For me, this fix has worked:
Click on "Copy internal link". Then paste the link into a note in Evernote. You now have a hyperlink with the name of the note, of which the link was copied. Since you pasted it within the Evernote application an evernote:/// link is created (if you paste anywhere else the link starts with www.evernote.com. Right-click the link you pasted into an Evernote note, click on copy to add the evernote:/// link to clipboard.
No matter where you paste this link, on windows it will open in the Evernote desktop application.