Hi everyone,

I’m posting this because I’m having a serious problem with Zotero that has essentially made it unusable for my workflow, and I’d like to know whether other people are experiencing the same thing.

(( The problem ))
I work with PDFs that contain figures, graphs, diagrams, scanned images, and other visual content.

The original PDF looks completely normal. All images and figures are present.

However, once I make annotations in Zotero's PDF reader — even a simple highlight — and then use Save As / Export PDF, some of the images/figures in the resulting PDF are completely deleted.

They are not faded, low-quality, or slightly altered.

They are simply gone from the exported PDF.

(( The important part is that: ))

Original PDF → Save/Export without annotations: everything is present and looks normal.
Original PDF → annotate in Zotero → Save/Export: some images/figures are completely missing.
The original PDF itself is not damaged.
The problem appears specifically after Zotero annotations are added and the PDF is exported.
What I've tested
I initially thought this might be a Zotero 10 issue, so I also tested Zotero 9.0.6 with the same PDF.

Unfortunately, I get the same problem.

I also tested the exact same source PDF, so this isn't an issue with different versions of the document.

** (( Why this is a major problem ))
For me, Zotero's annotation workflow is essentially:

Read → annotate → export/share/archive the annotated PDF

But if exporting an annotated PDF deletes parts of the original document, I can't trust the exported PDF.

This is especially serious for academic papers where figures, microscopy images, plots, diagrams, and scanned material contain important information.

I need the exported PDF to preserve the original document exactly, with my annotations added on top.

** (( What I would expect ))

Ideally:

Original PDF + Zotero annotations = original PDF completely preserved + annotations

The existing page content should not be removed or modified.

Instead, I'm getting:

Original PDF → annotate in Zotero → export → some images/figures disappear

Questions
Has anyone else experienced this?
Is this a known bug in Zotero's PDF annotation/export system?
Is there a setting or workaround that prevents images from being deleted?
Is there a way to export/flatten Zotero annotations without modifying the original PDF content?
Is there an existing bug report for this issue that I can follow?

This is a serious issue for my workflow because I cannot use Zotero if it can remove content from the original document.