I think the problem is you’ve multiple copies of the same prototype and with the same name (not illegal but not recommended for reasons now apparent) and this is confusing the agent query as it tends to de-dupe it’s matches. So although you’ve 5 prototypes named “Phlegmatic”, the query only lists 1 match (as the other 4 as regarded as duplicates). We need a different tack. (Again use Outline so you can see children, descendants, etc., as map view only shows you a single container). Here’s one prototype copied 3 times:
All are prototypes - but separate prototypes as changing the colour of one doesn’t affect the others. So the same name for each really is confusing agents. I can see all 4 if I try to apply prototypes:
Our saviour here is Find. Click in the view (left) pane of your document window and press Cmd+F, a search bar like below appears. Click on the ‘Text’ button (leftmost in the search bar) and it deselects. this tell Find we only want to match note names. We type ‘Phlegmatic’ in the box as shown:
Now use the Return key and a Find result pop-over opens. Click onto the frame of the pop-over and drag it so it becomes a stand-alone window:
Double click on each item in the find list in turn and the outline should expand to show and highlight that item. If your outline is not at root level (i.e shows a breadcrumb bar in the view pane), clicking on find results will show the selected item and alter the scope of the view - you will see the contents of the breadcrumb bar change. Either way, you can review the different matching items. I would:
- Review each one once. Decide which is the ‘real’ prototype and make a note of where that lives.
- Re-visit the un-wanted prototypes and use the Inspector to un-tick them as prototypes and—importantly—give each a new unique name (and not something like “Phlegmatic copy 1” or you’ll soon be back in the same confusion).
- Close the Find result window and click the ‘done’ button on the Find bar to close it.
You should now have only one copy of the “Phlegmatic” prototype.
Without implying any censure, the above is a good example of why it’s a very good idea to try out new features you don’t yet understand in a new document and only add them to your real work once you’re confident. That way, if you mess up, you can just trash the test file and start over. If you need to use ‘real’ data, make a copy of you work file and name it something different; do this before you start working in it so you don’t experiment in your main work file. As with a new file if you mess up you can delete the file and start over without affecting your actual work and the hours of effort is represents.