You are not creating the PdfStamper object correctly. Using:
PdfStamper stamper = new PdfStamper(pdfReader, filledPdf, '\0', true)
In your code, you are not using PdfStamper in add mode. This means that iText will reorganize various objects in your PDF file. This is usually not a problem.
However: your PDF file is included using Reader, which means that your PDF code is digitally signed using a private key owned by Adobe. By reorganizing objects inside a PDF, this signature is broken. This is stated in the message that you already mentioned:
This document has included advanced features. This document has been modified since it was created and using advanced features is no longer possible.
You have modified the document in a way that is not allowed (see section 8.7 of my book entitled "Retention of Use Rights Forms Supported by the Reader").
In order not to violate the signature, you need to use PdfStamper in add mode. Instead of reorganizing the original content, iText will now save the original file unchanged and add new content after the end of the original file.
Bruno lowagie
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