Thanks a lot for looking into this.
I tied to add third parameter to getImportedPage so it looks like this:

 target.addPage( target.getImportedPage( source, i, true ) );


I am getting the following exception now:

Exception thrown
                BadPdfFormatException: No StructTreeRoot found, this probably 
isn't a tagged PDF document!(PdfStructTreeController.java:69)
Call stack
                
com.itextpdf.text.pdf.PdfStructTreeController.<init>(PdfStructTreeController.java:69)
                com.itextpdf.text.pdf.PdfCopy.getImportedPage(PdfCopy.java:263)
                
com.fmr.fic.ai.service.PDFGenerationServicejClassImpl.appendPDF(PDFGenerationServicejClassImpl.java:877)
                
com.fmr.fic.ai.service.PDFGenerationServicejClassImpl.generateStatementsFromXML(PDFGenerationServicejClassImpl.java:588)
                
com.fmr.fic.ai.service.PDFGenerationServicejClassImpl.generateStatement(PDFGenerationServicejClassImpl.java:486)
                sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
                
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                java.lang.reflect.Method.invoke(Method.java:597)
                
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309)
                (124 more)

I checked PdfStructTreeController code, and have found that exception is thown 
by this line of code:

if (!writer.isTagged())
            throw new 
BadPdfFormatException(MessageLocalization.getComposedMessage("no.structtreeroot.found"));

In my case, writer is my PdfCopy object, and I used newPDF.setTagged(). Is 
something missing?

Thanks,
Alex

From: iText mailing list [mailto:i...@1t3xt.info]
Sent: Thursday, August 07, 2014 2:22 PM
To: itext-questions@lists.sourceforge.net
Subject: Re: [iText-questions] method PdfCopy.fixTaggedStructure throws 
NullPointerException

On 8/7/2014 10:39 AM, Pichtchikov, Alexandre wrote:
target.addPage( target.getImportedPage( source, i ) );

This line is wrong, you should add the boolean value that tells iText to 
preserve the structure.
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