Specifically I suspect the note belongs to a "Conflicting Changes" notebook, which gets automatically created a note you are trying to upsync conflicts with a copy already on the server. There might be other sync errors that trigger this as well.
If you look at the screenshot of the Mac app, the note belongs to a notebook that starts with "Con..." rather than something like "cherian's notebook" as seen in the screenshot from the Web app.
Users who run into this get a sync error and a modal dialog explaining that their copy of the note is placed into a local notebook titled, "Conflicting Changes [Date/timestamp]" There should be another copy of the note on the Evernote servers. It is possible that when Cherian saw this, he deleted the copy of the note on the Evernote servers and kept the local copy, which would be the opposite of what he'd want to do. (Total guess)
I would guess that this happened very early on and Cherian has been adding & editing this note locally in that local notebook, but not realizing it. The dialog can be a little confusing, and many of us just click away modal dialogs without thinking about it too much.
If you primarily ever work out of All Notes, you may not pay much attention to which notebooks your notes are in. Especially if you only edit that one note on the desktop. If you worked between desktop and mobile and/or web it would be easy to immediately notice that note missing entirely.
It is possible that there wasn't anything wrong with the note as the customer support agent said, but rather the note was just in a local notebook. Copy/pasting it into a new note would solve it in either case.
Local Notebooks exist only for the desktop clients. You can create one to put in notes you don't want sync'd up to the Evernote service. They're also a place to store notes if you're out of this month's quota.
Source: Customer Support agents escalate up to specialists, which eventually escalates up to Product Management. Almost exclusively with really weird and hairy problems.