Hello. I'm adding to this thread because I am experiencing a similar issue. I hope that is okay.
I use Zotero on my PC and also use the Zotero for iOS on my iPad. I recently added a citation with PDF to my library through my PC. Everything synced and I was able to open the PDF on my iPad where I added some annotations. I also added a note to the entry on my iPad. When I go back to my Zotero library on my PC the note has synced but not the PDF.
I checked in the online library I see both the note and the PDF have synced from the iPad but for some reason the PDF is not being pushed to my PC library.
I'm not sure what you mean by "I see both the note and the PDF have synced from the iPad but for some reason the PDF is not being pushed to my PC library"? You added the PDF on your PC, so it would obviously exist there already. Are you referring to annotations you made? (Those are synced separately from the PDF itself.) But you see them in the online library? If so, this has nothing to do with the iPad.
I use Zotero on my PC and also use the Zotero for iOS on my iPad. I recently added a citation with PDF to my library through my PC. Everything synced and I was able to open the PDF on my iPad where I added some annotations. I also added a note to the entry on my iPad. When I go back to my Zotero library on my PC the note has synced but not the PDF.
I checked in the online library I see both the note and the PDF have synced from the iPad but for some reason the PDF is not being pushed to my PC library.
I'm not sure what you mean by "I see both the note and the PDF have synced from the iPad but for some reason the PDF is not being pushed to my PC library"? You added the PDF on your PC, so it would obviously exist there already. Are you referring to annotations you made? (Those are synced separately from the PDF itself.) But you see them in the online library? If so, this has nothing to do with the iPad.
In general, see Changes Not Syncing. But where are you looking for the annotations? In the built-in PDF reader or in an external PDF reader? They won't appear in an external PDF reader.
The issue has to do with using the built-in PDF reader for annotation. Something I discovered shortly after posting. Sorry to waste your time.