Hypothesis unifies annotations across copies of PDFs based on a "fingerprint" (unique ID) that is created by authoring tools. The fingerprint persists across copies of the same document, but not across variants. So if you have two documents that look the same but are not cross-anchoring annotations, check to see if the fingerprints match. To do that with Hypothesis:
- Load the PDF into Chrome (e.g. by dragging it from your computer's file viewer into Chrome)
- Open Chrome's Customize and Control menu (upper right, vertical triple dots)
- More Tools -> Developer Tools -> Console
You'll see something like this:
- PDF fcfbb33577a82236301d15889a77df36 [1.3 Mac OS X 10.12.3 Quartz PDFContext / Adobe InDesign CS2 (4.0.5)] (PDF.js: 1.1.215)
The fingerprint in this case is fcfbb33577a82236301d15889a77df36. Check that it matches in both documents.