Thanks for moving the discussion @DTLow. Apologies, I was not aware of the Mac Feedback forum.
Confirming: when I click on the Helper, I get a floating dropdown scratchpad appear, with various options selectable at the top. I choose the 3rd one (icon: iMac with cross-hairs on it), which allows me cross-hairs to select a region of my screen. Then I click the "Save to Evernote" button on the dropdown, and the clipping 'disappears'.
In the past, when I open Evernote on that same machine, voilà, all my clippings since I last opened Evernote are visible in my default location/folder/notepad within Evernote.
But since the bug appeared, my default clipping location is completely empty. However, if I now repeat the above clipping steps (with Evernote open) I get the newly saved clipping AND all_my_previously_freshly-clipped_but_now_invisible_clippings_since_I_last_did_this suddenly reappear in that default location, exactly as they should have done, *except* now only in batch.
And if I do helper clippings and save, then open Evernote (with the default clipping location apparently empty), and this time I don't do clippings with Evernote running, then the clippings remain invisible and there is no way of knowing there are clippings that have been made since Evernote was last opened.
I don't know the exact date when this behaviour changed, but it's been about a month (i.e. late 2017).