I tried this code on the 3.0 version on the SourceFailure.pdf file.

        PDAcroForm acroForm = doc.getDocumentCatalog().getAcroForm();
        List<PDField> list = new ArrayList<>();
        for (PDField field : acroForm.getFieldTree())
        {
            list.add(field);
        }
        acroForm.flatten(list, true);

and after saving I got a fully flattened file. Please try that with 2.0.24. Your zip file needs us to analyse > 500 lines of code and set up a project with dependencies.

Tilman


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