Hello AstroHao,
Thanks so much for your reply! Yes, I read exclusively academic literature (accounting and finance) in pdf files.

I assume what I should conclude from your reply and the links your provided is that PDF Expert is not a reliable interface with Zotfile? When you say you're using the "official PDF reader" are you referring to something integrated with the new Zotero beta app for IPad? I have not ventured into that yet. My desktop Zotero does not have a pdf reader that I can identify; the Zotero pdf files open in my Adobe Pro 2020 software when I am on my desktop, and I transfer files to and from an IPad for detailed annotation.

Thanks to your email, I have used Adobe Reader on the IPad exclusively today, and the annotations seem to be extracting properly into Zotero. My objective is to extract searchable highlights and comments/notes to Zotero. Why Adobe cannot make annotating as user friendly as PDF Expert is beyond me. If you see this post and can clarify what you meant about the "official PDF reader" I would appreciate it and I'll watch for a response.

Good luck with your work, and thanks again for your help!

Sorry for the ambiguity. I meant the adobe series, the Adobe Acrobat or Reader. Since adobe sets and holds the standard for the PDF, I used to refer to it as official... I also edited the above reply to clarify this.

If you just use highlights and underlines, may also adding notes, adobe is acceptable.

I transfer files using Dropbox. Abode reader on Android platform can direct edit the files in Dropbox, which is a very convenient feature and also a plus for the adobe reader app.

@astroHao: That's addressed on the linked page:

Annotations are stored in the Zotero database, not in the PDF file, which allows for much more advanced functionality as well as fast syncing. The File menu contains a new option to export PDFs, which will convert any Zotero annotations into standard annotations in the exported file. (An upcoming version will let you omit annotations, but in the meantime you can drag files to your filesystem to copy just the file.) Similarly, when exporting metadata from your library, there's a new “Include Annotations” option under “Export Files”. We plan to support other ways to export annotations in future updates. Your annotations will never be locked in Zotero.

Astrohao, thanks for the update! Ok, good to know that Adobe is working for you because I am investing loads of time reading & note-taking right now. I hope all my work will be extracted and contribute to several summer research projects. I’m very sad to give up on PDF Expert, but happy to have the problem solved.

Thank you, DStillman, for the information about the Beta. I am anxious to try it, but want to get functional with Zotero 5 before jumping into the fun, new beta.

I look forward to the beta pdf reader, too, but frankly one of the most valuable traits of Zotero is the ability to work with annotated files from external readers. It feels very safe to have cross-platform files, especially when investing a lot of time into the annotating, and even though handwritten notes don’t extract, they are right there in the Zotero-organized pdf file for reference.

I’m new to this but Zotero really is amazing! The only other place I’ve seen this ability to extract highlights is a beta importer from Readwise which is far less functional. The annotation integration really converts Zotero from a citation manager to a knowledge management system. I’m crossing my fingers that Adobe extractions continue to work as well as they did today, and once I have the process down, can’t wait to test-drive the new beta.

DStillman, the description is very helpful, good to know about the mobility because that is important to me, too - mobility of the notes allows for integration with several other trending apps, or even just filtering and reorganizing notes in Excel or something. The ability to export annotations will be really valuable for organizing notes for writing. I can't believe I've been missing all this until now!