I have the exact same issue. My notes taken at the helper app at the Mac Menu bar disappeared after clicking "Save to Evernote" and not able to sync to Inbox of Evernote. Despite Evernote for Mac running and repeatedly clicking Sync.
This has been bothering me a lot in the past 6 months, as I use Helper on the Menu bar a lot to jog down important notes. I used to be Premium user and moved to OneNote on Mac, but like Evernote more from UX perspectively. This has me put off forking money to Evernote since it's been there for the last 6 months without any updates.
From Chris notes above I discovered I need to create another dummy notes from the helper and then both the dummy notes and my previous notes will re-appear. But I have wasted so much time and efforts before trying to find these disappeared notes.
Running Evernote on Mac (Version 7.5.2 (457164 Direct))