Which app did you use for highlighting?
I used DevonThinkPro.
Does it work if the PDF document is selected in the main view (e.g. icon or list view)?
Yes! Thank you. I closed the window with the open document and selected tools | summarize highlights | as markdown. That produced a markdown file, which I can now edit.
Does the document in the open window always have to be closed for tools in DevonThink to work?
Most tools are applied to the selection of the main window.
That makes programming sense to me, but could you add a message if no file is selected in the main window?
The menu items should actually be disabled in this case.
Sure, but my experiences suggest users might not know tools only work with selected files. The potential for user confusion would still remain… 
But with what would tools work if not with selected files? All of them?
The topmost open document? Or, an earlier idea, provide a message that the tool only works when a (single?) document is user selected.
If a document is open, it would be visible in the view/edit pane and the tools would be enabled and working. Or are you referring to something else?
The documents were open in the view/edit pane, but the tool did not start, nor was there any message upon clicking the tool | summarize highlight | . As I understood @cgrunenberg, the tool only works with a (single–this is still unclear to me?) file selected in the main view.
And I will amend my statement… the Summarize command works on the selected item in the item list. This can even be more than one document. However, something must be selected in the item list. This is what @cgrunenberg was referring to.
This will not work…
This will…
Exactly. But If a user selects the tool with nothing selected (your first image) there is no message whatsoever…
I think there should be a message in this case. That’s a UI issue beyond this discussion, but I’ll be brave and suggest “No file selected”. A corresponding explanation in the documentation should cover the scenario I had well–at least, I think so 
Sorry to rehash an old thread. Is there a placeholder I can use to perform the “insert summarised annotations” command in the inspector’s annotations area?
I have template RTF annotations I would like, but I also really like the summarise annotations function. However, you can’t have both, it seems once I begin a template annotation from inspector, the “insert summarised annotations” option is no longer there. Vice-versa if I start with a summarise annotations option.
I see there is an “annotations count” placeholder, but that only produces a number (how many times I’ve annotated the PDF/document).
I know that there is an “insert quote” feature on the inspector annotation which I could use with an already created template, but that would mean having to go through all the quotes on each document.
- On a separate note, perhaps another thread, but can this command be placed in the contextual menu? It’s might be smoother than having to perform the command from the inspector every time.
What kind of template did you use? As long as it’s Markdown or RTF(D) the command should be available.