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I got quick reply from Robyn at Omni (thanks Robyn!) to fix it like this:

"Select the Stencil window and then go to View>Show Toolbar from the top menu bar."

It worked, though I'm not sure how it got in that state - there doesn't seem to be a shortcut-key-sequence to toggle that, and it isn't in a part of the menu that I would have stumbled on accidentally.