Articles on: Support & Troubleshooting

I'm missing all my Layers — Lost Layer recovery

If your Layers with annotations have disappeared — usually after a Scriptation script was opened in another PDF app — your work is almost certainly still there in a Lost Layer. Scriptation creates Lost Layers as a safety net when its Layer metadata has been damaged. Your annotations aren't deleted; they're just hidden, and they're recoverable.


Why this happens


When you open a Scriptation PDF in another PDF app — Apple Preview, Adobe Acrobat, GoodNotes, Adobe Fill & Sign, etc. — that app saves the file in its own format. If the modified file then syncs back to the cloud, it can overwrite the original Layered version. The result: Scriptation opens the file and shows a blank or partial annotation set, even though your work is still there.


Recovery — Option 1: Restore an earlier version from cloud storage


If the file lives in Dropbox, Google Drive, or OneDrive, restoring the previous version is usually the cleanest fix. The version history goes back to before the other app touched the file:



📝 NOTE: iCloud Drive doesn't keep a file version history the way Dropbox / Google Drive / OneDrive do. If your file was in iCloud or stored locally (On My iPad / iPhone), skip to Option 2.


Recovery — Option 2: Lost Layer recovery in Scriptation


This pulls your hidden Layers back into view without needing a cloud restore. Use this when version history isn't available, or as a follow-up if the restored version still shows missing notes.


⚠️ IMPORTANT: Before you start, make a copy of the script so you have a safe starting point.


  1. Make a copy of the script first:
  • Tap the 3-dot menu (⋯) next to the file name;
  • Choose Copy;
  • Tap Select to make a local copy;
  • Rename the new file (for example, "Filename — copy").


  1. Open the copy of the script.


  1. From the Top Toolbar, tap Layers. You may see only one Layer:



  1. Tap the 3-dot menu at the upper right of the Layers sidebar and choose Duplicate:



  1. You may now see one or more Lost Layers appear:



  1. Tap the closed-eye icon on a Lost Layer to make it visible, and check whether the missing annotations are there:


✅ TIP: You can also see what's in a Lost Layer via the Annotation Outline — tap the Outline icon (the open book) on the Top Toolbar and switch to the Annotations tab.


Next steps after recovery


  • If the Lost Layer has annotations you need, merge it back into another Layer to keep them organized;
  • If the annotations are duplicates of what's already in another Layer (or no longer needed), delete the Layer.


Prevention


⚠️ HEADS UP: Don't open Scriptation PDFs in other PDF apps. Even just viewing the file in another app can save changes back to the file and damage your Layers.


If you need to send a flat PDF of your script to someone outside Scriptation, export a copy from inside Scriptation instead of opening the original in another app — see How can I share my notes or email my file?


If this doesn't work


If you run into trouble or need help with the process, use the Send us an email button at the bottom of this page. Please attach your script and any details that'll help us solve the problem — including which other app opened the file and which cloud provider stores it.


What's Next


How to Merge Layers
How to Delete a Layer
I can't find missing notes. What can I do?
How can I share my file with Scriptation's Support team?

Updated on: 25/06/2026

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