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, 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.

Flattening usually happens when the script was opened or re-saved in another PDF app, or processed by a watermarking 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.

How to confirm your PDF is flattened

Try using the Text Highlight tool on a line of dialogue or action.

• 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 the clean draft into Scriptation.
3. Run Note Transfer again from your annotated old draft to the new clean draft.

What's Next

How do I transfer my notes?
What is a flattened PDF?
Text Highlight vs Highlighting with the Marker
I'm missing all my Layers — Lost Layer recovery

Updated on: 21/07/2026