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For an electronic publication of my thesis I need to remove two chapters due to copyright restrictions. However, I would still like to have everything else look exactly the same (table of content, list of figures, tables, ...).

At the moment, I create a second version of the PDF in which I replace the content of the corresponding pages:

\newpage Content not included due to copyright restrictions. Please refer to the original article in ...

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As this affects the table of content and the lists, I merge parts of the original document and the new one to the final one:

gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dFirstPage=1 -dLastPage=53 -sOutputFile=output_01.pdf thesis.pdf
...

#merge all files
gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=thesis_blackened.pdf output_01.pdf output_01_black.pdf output_02.pdf output_02_black.pdf output_03.pdf

The result I get is almost exactly what I need.
Unfortunately, the listing of the structure and the hyperlinks are a little messed up.
Is there a way of not showing content of a latex file in the PDF but still consider it in the listings?
Another option I can think of would be to use some other program to erase the content in the thesis PDF itself.
Is there another solution you could think of?

Green
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    So, you want the “forbidden part” to contribute to the table of contents, list of tables, list of figures, etc., even in the “public” document? Won't such leaks of copyrighted material constitute a copyright violation? ;-) I haven't tested with hyperlinks, but a tool such as pdftk (command line) or pdfarranger (graphical interface) allows one to remove pages from a document and insert pages from another one. Not sure it will work better than what you did with gs, though. – frougon Jan 26 '20 at 12:01
  • It is ok for me to insert this content without copyright violation. I could even include a full version of my papers that is similar to the final one. However, in this case it does not make sense as I want to upload my thesis and rather have things removed than having something included that is not equal to the printed one. I might just test your suggested tools and see what result I get with them. – Green Feb 01 '20 at 08:57

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