> ## Knowledge Base Index
> Fetch the complete knowledge base index at: https://help.scriptation.com/sitemap.xml
> Use this file to discover available pages before exploring further.
> Pure-Markdown content can be obtained by appending a '.md' suffix to the content URLs listed in the sitemap (without the trailing slash).

# Why are my annotations missing after Note Transfer?

If your **manual annotations** — highlights you drew by hand, notes, drawings, text marking, or stamps — didn't transfer to your new draft, the most likely cause is a flattened source PDF. When a PDF has been [flattened](https://help.scriptation.com/en/article/what-is-a-flattened-pdf-p2vq4m/), Scriptation can no longer read the underlying text — and Note Transfer relies on that text layer to figure out where text-anchored annotations belong on the new draft.

|| 📝 NOTE: Auto-Highlight (Highlight icon on the Top Toolbar) regenerates per draft — it doesn't transfer. Manual highlighting (Highlighter tool in the Annotation Toolbar) transfers with your other notes.  For Auto-Highlight, see [Auto-Highlight doesn't carry over to new drafts — here's why](https://help.scriptation.com/en/article/why-didnt-my-character-or-scene-auto-highlighting-transfer-u83v8z/).

Flattening usually happens when the script was opened or re-saved in another PDF app, or processed by a [watermarking](https://help.scriptation.com/en/article/how-does-scriptation-handle-watermarks-1vpgkm5/) tool before it reached you.

##### Which annotations are affected

Anything that anchors to specific text in the script won't transfer from a flattened source:

* **Freeform Pen and Highlights** — any marker strokes placed over text;
* **Text Highlights, Underlines, Strikethroughs, Squiggles** — Text Marking tools that lock to text;
* **Shapes** — lines, arrows, ellipses, and rectangles;
* **Sticky Notes anchored to a word or line of dialogue.**

|| 📝 NOTE: Annotations that don't depend on the text — such as **drawings**, stamps, or s**ticky notes** placed in the margin or on a blank area — may transfer normally even to/from a flattened PDF.

##### How to confirm your PDF is flattened

Try using the [Text Highlight](https://help.scriptation.com/en/article/how-do-i-use-the-text-marking-tools-highlight-underline-squiggle-and-strikethrough-5i7wnp/) tool on a line of dialogue or action.

![](https://storage.crisp.chat/users/helpdesk/website/60818aeea8717000/img72a86fc28959-1_1wxigls.jpeg =700x42)

* If the highlight **snaps to the text** — your PDF is fine, and something else is going on. Use the **Send us an email** button at the bottom of this page with the files so we can take a look.
* If the highlight **doesn't recognize any text** — your PDF is flattened. Text-anchored annotations can't be transferred from a flattened source.

##### How to recover

1. Ask your production folks for an **un-flattened, text-based PDF** of the same draft. (Most screenwriting programs export this by default — it's flattening or scanning that breaks it.)
2. [Re-import](https://help.scriptation.com/en/article/how-do-i-import-scripts-into-scriptation-k34r8d/) the clean draft into Scriptation.
3. Run [Note Transfer](https://help.scriptation.com/en/article/how-do-i-transfer-my-notes-1khpcd8/) again from your annotated old draft to the new clean draft.


||| ⚠️ HEADS UP: If your annotations look like they vanished *entirely*, see [My note transfer didn't work. Help!](https://help.scriptation.com/en/article/my-note-transfer-didnt-work-help-tqir96/) for more solutions. 

# What's Next

[How do I transfer my notes?](https://help.scriptation.com/en/article/how-do-i-transfer-my-notes-1khpcd8/)
[What is a flattened PDF?](https://help.scriptation.com/en/article/what-is-a-flattened-pdf-p2vq4m/)
[Text Highlight vs Highlighting with the Marker](https://help.scriptation.com/en/article/text-highlight-vs-highlighting-with-the-marker-13tyfuj/)
[I'm missing all my Layers — Lost Layer recovery](https://help.scriptation.com/en/article/im-missing-all-of-my-layers-1q3wawc/)