I have a PDF book in Devonthink. Well many of them actually.
I’ve been trying to figure out how to highlight within Devonthink and still be able to get the highlights out. And it seems possible if I highlight within Devonthink then open the PDF document in Highlights. It shows me all of the highlighted places that I can an export if I want to.
The issue is, every time I try and highlight some thing, it works but then I get a spinning ball that forces me to wait before I do anything. That shouldn’t be happening. I’m not sure what I’m doing wrong and couldn’t find nothing regarding this in the manual.
Another strange this is if I try to highlight the first sentence on a page of the PDF, it turns the whole page brown and then does make the highlight. Again, I get the spinning ball. It only does this strange behavior on the first sentence of a new page.
I have tried restarting Devonthink and behavior continues.
DEVONthink 3.9 and macOS 13.2.1 (both latest)?
Monterrey latest. My Mac pro trashcan is too old for Ventura.
Devonthink 3.9 yes.
Check the DEVONthink Log for clues? Use Apple Preview works on those PDFs? (if same result, issue might be the PDFs).
DEVONthink staff might have other debug or support suggestions.
And what size / how many pages is this PDF?
It is 103 pages.
There is nothing in the log files regarding this.
The problem also exists in Apple Preview, leading me to believe it is the document.
I did reconvert this and OCR it again and it does work better now. Still has some issues. But I believe it is the document since I have tried others and they don’t seem to have the same problem.
By the way, for anyone who wants to know, I found something very useful. You can mark up the document in Devonthink. Then you can open the document in the Highlights app and it will show you all of the highlights on the right hand side. You can then export those and send them back to Devonthink so you have just your highlights in notes. It is super system. At least I have experienced this with one document. We’ll see if it continues on like this but it is a real breakthrough for me using this.
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You know you can do this in Devonthink? You don’t need to export to Highlights to do it.
Once you’ve marked up your PDF in DevonThink, go to the top nav bar and Tools > Summarize highlights > Markdown [or whatever format you prefer]. It will create a file in the same location as your PDF with all your highlights and notes, with links.
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This is a good investigation approach. 
If you’d like to ZIP and send us the PDF via a support ticket we could see if the behavior happens here too.
I did not know that. That is fantastic. Thank you for sharing it and I can’t wait to begin using it.
Thanks. I appreciate it. So far I don’t see it repeated and in all of my devices it does the same thing. I have it on my Mac, iPad, and iPhone. So I can really only assume it is that PDF. But if I see it happening more, I will definitely send you one.
Thanks for the offer.