“Is it possible to partially flatten the PDF or another way to display the data?”
Yes, sort-of… rather than using the plugin’s flatten function, you can set individual PDF form fields to “Read Only”, the merge will still work but users won’t be able to edit the “read only” fields.
“The form was created using Adobe LiveCycle Designer”
Our plugin is not compatible with LiveCycle forms, you’ll need to convert the form to an Acrobat Form. We found PDFEscape.com to be a useful tool to convert LiveCycle forms to regular Acrobat Forms. Simply upload it, unlock one field to allow editing, then download the PDF. Done. Upload to PRO2PDF and all should work as expected.
We remain at your service.