I found this thread because I had a similar occurrence. I also employed an easy fix, which may not work for everyone, but if it does, you're home free.
Here's what happened to me:
This morning I updated my Weekend To-Do note in Evernote on my desktop PC. It's a long note, probably the first I ever created. I synced it, then shut down my PC. At lunch I wanted to show a friend how cool Evernote is. So I pulled up my Weekend note and to my chagrin, it appeared it hadn't synced, or perhaps that my iPhone wasn't syncing with Evernote. Then I recalled how Evernote sometimes fumbles the sync and scrolled down . . . down . . . down. Sure enough, there was the "Conflicting changes" notice, with my updated note (just a long below it). This is a royal pain to fix on an iPhone, so I put my phone away until this evening. I tried using iOS' select and delete feature and managed to delete the entire note, how I'm not sure (no, I did not choose "select all"). I opened my iPad, and of course it synced right away to my iPhone -- Poof! Weekend note gone.
Here's the simple solution: Recalling that the note was last updated on my desktop PC, and hadn't been changed since then (apart from the inadvertent deletion of all text on the iOS devices), I went downstairs, disconnected my network cable from my desktop PC so it could not sync, fired up the PC, and opened Evernote. My local copy of my Weekend note was, of course, still there, and going nowhere. I simply chose the "Duplicate Note" feature, gave the duplicate a new name ("Weekend (new")), plugged the network connection back in, and synced Evernote. The old Weekend Note went Poof! again, but it didn't matter since the entire content was now preserved in a new identical (except for the note's title) note. So I deleted the old note, synced again. exited Evernote, and then opened it on my iPhone and iPad, where they sync worked, leaving the new note with the old text, and deleting the old note with the text deleted. Problem solved!
I realize you have to be a little lucky for this to work for you, but since from reading posts this often happens because the iOS is so kludgey with its select and delete text, it may help someone out who hasn't thought to do this.
I agree, Evernote needs to build in an undelete feature that can easily revert the last 10 changes. It's easy code, and the premium "Note History" feature doesn't do this, and really isn't worth the price.