Flattening PDF with Acrobat 11

Dear Experts,

I have been asked to help our medical writer with one of the documents, which is a PDF file with annotation.  For the submission, she is required to flatten the file, but when she does, some of the annotation goes away.  It seems strange that it works for most of the portions, but some are totally gone, are misplaced.  Please advise.
yballanAsked:
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Joe Winograd, Fellow&MVEDeveloperCommented:
Some questions:

(1) Is her Acrobat XI the Pro or Std edition?

(2) There are numerous ways to flatten a PDF. Exactly how is she flattening it?

(3) Which type of annotations are gone or misplaced? Sticky notes? Highlights? Text? Etc.?

Regards, Joe
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yballanAuthor Commented:
Dear Joe, Thank you for a quick response.
1)  It is Pro
2)  We go to Preflight, then do "flatten annotations and form fields"
3)  The annotations are text inside a box, box is there but the text is gone.  Another type is highlights move to another part of paragraph.
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Joe Winograd, Fellow&MVEDeveloperCommented:
> text inside a box

I presume you mean the annotation that Acrobat XI Pro calls a Sticky Note. I am not an expert on Preflight (I never use it), but it's my understanding that Preflight's "Flatten annotations and form fields" shows only the icon for the Sticky Note and not the text in it. You could write JavaScript to do it (beyond my expertise) or install a third-party flattener, such as these:

https://files.acrobat.com/preview/37e3a885-b96e-457d-81dc-8d6c098fa114
http://abracadabrapdf.net/utilities-in-english/acrobat-utilities/abracadabratools_en/
http://www.pdfscripting.com/public/Free_Acrobat_Automation_Tools.cfm

Here's an interesting thread about it at the AcrobatUsers forum:
https://answers.acrobatusers.com/how-do-I-flatten-comments-in-Acrobat-XI-q146382.aspx

Also, here's a good article about flattening, although it applies to Acrobat X, not XI:
https://acrobatusers.com/assets/uploads/actions/Flatten_Fields_and_Comments.pdf

Another approach is to print to a PDF print driver that flattens. But to get the Sticky Notes, you need to tick the "Print notes and pop-ups" box in Edit>Preferences>Commenting (it is un-ticked by default):

Print notes
Also, you need to be careful about positioning the Sticky Notes so they don't overlay portions of the document. Here's an article that explains in detail the printing approach:
http://blogs.adobe.com/acrolaw/2010/06/prinitng_sticky_notes_and_other/

> highlights move to another part of paragraph

I can't explain that. I've never seen it happen, except when it is a scanned document that has both an image and the text from OCR. In that case, it is possible for the highlight (which goes against the underlying text) not to line up exactly with the image, but it is typically not far off — certainly not in another part of the paragraph. Regards, Joe
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yballanAuthor Commented:
Dear Joe,

Thank you for detailed explanation, after trying all, I found that printing the original PDF using Adobe PDF writer flattens and keeps annotations and highlights intact.  Unfortunately, I lost all of my bookmarks when I did that.  If I can retain bookmarks while printing to PDF, then I am all set!!!
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Joe Winograd, Fellow&MVEDeveloperCommented:
Yes, printing to Adobe PDF does not retain the bookmarks. A work-around is to save the bookmarks before printing and restore them after printing. This can be done easily via a single command with the PDF Toolkit (PDFtk), an excellent (free!) product that has numerous features to manipulate PDFs. It comes in both command line and GUI versions. The command line version is called PDFtk Server and may be downloaded here:
http://www.pdflabs.com/tools/pdftk-server/

Don't be misled by "Server" in the name. I don't know why they called it that, but it's just an executable (pdftk.exe, with a supporting DLL, libiconv2.dll) that runs on XP, Vista, W7, and W8 (i.e., it does not have to run on a "server" OS).

This one line will save the bookmarks in a text file:
pdftk.exe InputFile.pdf dump_data output SaveBookmarks.txt

Open in new window

Now print using Adobe PDF. Then this one line will restore the saved bookmarks to the new PDF file:
pdftk.exe PrintedFile.pdf update_info SaveBookmarks.txt output NewFile.pdf

Open in new window

Put each of those in a simple BAT file (perhaps SaveB and RestoreB) and you should be all set. Of course, the input file could easily be a parameter — I hard-coded it just for illustrative purposes. Regards, Joe
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yballanAuthor Commented:
Wow, that's terrific, thank you!!!
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Joe Winograd, Fellow&MVEDeveloperCommented:
You're very welcome! Happy to help. Regards, Joe
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yballanAuthor Commented:
Dear Joe,

I just shared your advise with my co-worker, she and I are very excited to know this nifty tool.
Thank you!!!
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Joe Winograd, Fellow&MVEDeveloperCommented:
You're welcome! I'm glad you shared it with your co-worker. Also, if you and your co-worker do a lot of work with PDF files, you may be interested in another nifty set of tools called Xpdf. It is a set of nine utilities that perform various functions on PDFs. I published a series of three 5-minute video Micro Tutorials here at EE that discuss the overall library and two of the nine tools:

Xpdf - Command Line Utility for PDF Files - Part 1
Xpdf - Extract Images from PDF Files - Part 2
Xpdf - Convert PDF Files to Plain Text Files - Part 3

I hope you find the videos to be a worthwhile 15 minutes. Regards, Joe
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