I am having the same problem. Despite what "dstillman" and "adamsmith" are reflexively saying in defense of Zotero, it is obvious that their reply is at best highly biased.
If I highlight a pdf document outside Zotero the highlights are saved without any problem. It is only when I try doing it after they are in Zotero that the problem - after I just lost all my notes on a specific document, I am much more inclined to using similar services - even if clunkier - for the peace of mind of not having to deal with these issues.
Zotero 6 stores PDF annotations in the database — if you're creating these in the Zotero PDF reader, you won't see them if you open the PDF in an external program unless you export the file.
If you're talking about saving annotations in an external reader, there's no "defense of Zotero" here — we just literally have nothing to do with how an external reader saves annotations. If you've set Zotero to open PDFs externally, all it does is open the file in the external app. If annotations are saved back to the file, Zotero will sync the locally modified file back up to the Zotero servers if you're using Zotero syncing.
Upgrade Storage
If I highlight a pdf document outside Zotero the highlights are saved without any problem. It is only when I try doing it after they are in Zotero that the problem - after I just lost all my notes on a specific document, I am much more inclined to using similar services - even if clunkier - for the peace of mind of not having to deal with these issues.
Zotero 6 stores PDF annotations in the database — if you're creating these in the Zotero PDF reader, you won't see them if you open the PDF in an external program unless you export the file.
If you're talking about saving annotations in an external reader, there's no "defense of Zotero" here — we just literally have nothing to do with how an external reader saves annotations. If you've set Zotero to open PDFs externally, all it does is open the file in the external app. If annotations are saved back to the file, Zotero will sync the locally modified file back up to the Zotero servers if you're using Zotero syncing.