I have the same problem. I have a budget XLS, where I paste the link to (e.g.) an invoice, which has been uploaded to Evernote, into that XLS beside the amount. This used to work perfectly fine until recently:
Upload invoice to Evernote via Scannable
Move it into the correct Notebook, add keywords etc.
Right click on that note, select "copy internal link"
Jump over to the XLS, Paste the clipboard content (i.e. the link) into the correct cell. There, it displays as the title of the note with a link behind it, so I can jump straight from Excel into that note in evernote.
Since the latest Evernote version, on right-licking the note title (Step 3 above) and selecting "copy internal link" I have to select between two types of link, whichever I choose, when I copy it into Excel, it is displayed there as evernote:/// link, with NO link behind it.
However, the roundabout way described above with an intermediate step via another note works, albeit clumsily. Thanks for that.