My PDF highlights made using the Devonthink PDF app on the Mac are not synching from Devonthink to Devonthink to Go on my iPad. The PDF shows up on the iPad without the highlights. It does work the other way around: highlights done in Devonthink to Go on the iPad do synch to Devonthink on my Mac.
What is the problem?
Thanks.
We are investigating this. Thanks for your patience and understanding.
I am having this problem as well, any progress?
Not to keep piling on, but I am experiencing the same problem. I am using the latest versions of DTPO and DTTG on Mojave.
Just to add some further context, I am seeing this as well – but still running macOS 10.13.6 (High Sierra), with DTPO 2.11.3 & DTTG2 2.7.1 (16337).
Just to pile on things. Highlights from DT3 don’t sync to DTTG. 
The problem is that the annotations created by macOS are not compliant to the official PDF standard. DEVONthink To Go, however, sticks to the standard and its PDF library does, at the moment, not show these annotations. As we’re not making this library there is little we can do here we’re afraid. We are in talks with the makers of the PDF library, though.
Just to be clear - highlights made in DTTG2, they do sync back/are being seen in DT3, correct?
Yes, you should see highlights made in DEVONthink To Go in DEVONthink on the Mac.
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And highlights made on the Mac sync to DEVONthink To Go but are just not shown.
Many thanks.
Hi @eboehnisch and @BLUEFROG,
It seems that this sync problem is true to me at this moment, so I suppose that it is still an issue.
I would like to hear your thoughts about adopting the SkimNotes framework.
I am glad that Devonthink is able to read Skim Notes, but what about writing? I came across Devonthink because this feature and this same feature was the main reason I recently made Devonthink the center tool of my research workflow.
It is true that I might be biased in my thoughts, but writing using the SkimNotes framework could be included as an option on both platforms and (hopefully) be an alternative solution to many.
As far as I know, there is no iOS app that can read Skim notes. Maybe this would be an appealing feature to many researchers.
What do you think? 
Welcome @rflcrz
While we are aware of Skim’s approach, it is proprietary. It’s an interesting suggestion but there are no current plans to support writing Skim annotations.
Is this problem solved yet? What’s the recommendation to highlight on MAC that will sync & show up on DTTG?
Addition: The Skim framework is exclusively designed for macOS and does not work on iOS (at least not out of the box).
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Very unfortunate that so long after this was reported there’s still no fix. I’ve been looking at DevonThink today purely to create a workflow for annotating PDFs and organizing them. Reading and annotation on an iPad is central to that. Oh well. I’d hoped I’d found a good tool.
Welcome @mikecohn
You can annotate PDFs in DEVONthink.
You can also annotate them in DEVONthink To Go with the in-app Pro Pack (see Settings > Manage).
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Thanks for replying. I’d already purchased but Pro Pack.
However, the problem is that annotations are not entirely compatible between your two products. If I add a note in DTTG I cannot see that note in DT. It’s saved in the file because if I export the PDF from DT and then open it in Acrobat, I can see the annotations.
Specifically what I’m trying to do is read a pdf on my ipad, highlight parts in yellow and sometimes add a note to the highlighted parts. Those notes made in DTTG do now show in DT.
Please let me know if there’s a workaround for this bug. If not, hopefully it’s on the list to be fixed but this thread made it sound like it’s been here for a couple of years. Thanks.