I have the problems with documents that I open in PDF Viewer directly from the DTTG file storage. Annotations are not saved.
When I open the same file from the Nextcloud file storage and edit it with PDF Viewer, the annotations are saved.
I have heard back from Readdle support (perhaps they have been in touch with you as well). They have been able to reproduce the issue and have filed it in their issue tracking system. It may take a while to be fixed, of course, but it has now been noted and acknowledged.
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Thank you very much poking them too. Weāve also received a confirmation that they have opened an internal ticket.
greatā¦ please let us know here as soon as it is fixed
Quick update: The Readdle engineers have now requested detailed information about how DEVONthink To Go provides the files to the Open In mechanism. We have just provided them with a description of what our app does and maybe they either find a flaw that we can correct or gain other insight into why it doesnāt work with PDF Expert (and maybe other apps too).
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Just a further update. I have updated PDF Expert on iPad to the new version 7.4.18 released yesterday and still no fix from Readdle.
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Yesterday I contacted with Readdleās customer support regarding this issue, but the guy responded that āat the current moment, PDF Expert doesnāt support DEVONthink integrationā and he has saved my request in āfeature wish list for future app updatesā. Besides, he suggested me to āmake a copy to PDF Expert > make changes (editing/annotating etc.) > then copy to Devonthinkā.
This is 
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To us they confirmed that itās an issue in PDF Expert but it āmight take them a while to fix itā.
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Thanks for sharing this interaction with Readdle on this issue.
Has anyone got any updates on this? It still doesnāt work on my ipad. PDF Expert isnāt crashing anymore but annotations made in PDF Expert canāt still be seen in DTTG 3.
No, still not working for me either. Itās a shame Readdle does not consider this to be worth fixing for six months. 
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I works for me with PDF Viewer by PSPDFKit, which works very well in the free version with annotations.
Lost a lot of work today because of this issue (PDF highlights not synced back, closed the PDF, highlights gone). No blame on DT, shouldāve checked it first. Still, very disappointing that this issue has not been fixed by Readdle. 
Edit: On the other hand, Iām glad that Iām neither insane nor too stupid to use it properly. 
Itās a shame that this has not been fixed by Readdle in over a year now but as some other PDF readers are also having interoperability issues on iOS/iPadOS with DEVONthink (and possibly other apps), perhaps the issue is not that easy to fix or it may have something to do with the OS itself and how it handles files sent and shared between apps.
Given the current situation, Readdle probably has enough on their hands right now, I just hope they are safe and bugs will be taken care of eventually hopefully. I still find PDF Expert to be best in class, and I am generally happy to annotate and work on PDFs in DTTG anyway.
Foxit works well, at least it did last time I tested it, if you are for some reason looking for an external app to annotate your PDFs in addition do DTTG.
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100% agree to everything youāve said! At the moment, I just hope everyone at Readdle is safe. And after a long journey trying all kinds of PDF editors, I intend to stick with PDF Expert as it is, as you have mentioned, best in class. And it works on macOS, too. So, I guess, Iāll use DTās own mark-up capabilities on my iPad and PDF Expert on the Mac.
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Well Iām glad my PDF Expert subscription is about to expire so I can make the switch to Highlights. PDF Expert iCloud sync has always been wonky for me.
Welcome @beglitched
Wishes for much less wonkiness with Highlights 
I donāt think Readdle (or anyone else for that matter) has any influence on when iCloud does its sync thing.
Iāve had issues with multiple apps every now and then (and these issues are usually solved on Macs with killall bird in Terminal to clear the iCloud Drive queue) and thatās usually down to the inherent wonkiness of iCloud and not the app developersā¦
I hope Highlights works better for you of course.
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That would be the same workflow I have thought of in the current situation.
Does this work well for you? Are there any issues appearing when mixing up the highlighting feature of PDF Expert (Mac) and DTTG (iOS) in the same document? Can you flawlessly continue highlighting on your iPad with DTTG after you started highlighting the document on your Mac with PDF Expert and vice versa?
For me this works flawlessly. I am also still waiting for Readdle to fix the issue with its iOS version. Currently I use PDF Expert on my Mac and DTTG on my ipad to annotate, etc. So annotating something in PDF Expert (Mac) and annotating the same file in DTTG is no problem.