Ubuntu – Where does okular store pdf annotations

The answer as of now is No.

This file is encrypted and can only be opened with Acrobat Reader.

richard@ubuntu:~/Desktop$ pdfinfo n-400.pdf 
Title:          Appication for Naturalization
Author:         USCIS
Creator:        Adobe LiveCycle Designer ES 8.2
Producer:       Adobe LiveCycle Designer ES 8.2
CreationDate:   Thu Nov 15 16:21:11 2007
ModDate:        Tue Jun 21 11:36:34 2011
Tagged:         yes
Pages:          1
Encrypted:      yes (print:yes copy:no change:no addNotes:no)
Page size:      612 x 792 pts (letter)
File size:      110428 bytes
Optimized:      no
PDF version:    1.7

The only unencrypted element is the following text, found using pdftotext

richard@ubuntu:~/Desktop$ pdftotext n-400.pdf l.txt && cat l.txt 
To view the full contents of this document, you need a later version of the PDF viewer. You can upgrade
to the latest version of Adobe Reader from www.adobe.com/products/acrobat/readstep2.html
For further support, go to www.adobe.com/support/products/acrreader.html

There are lots of people affected by this.

My solution was to install acroread, fill in and print the form (the option to save wasn't available either for the form I was using), and then remove acroread.

Poppler PDF library can do this - Okular and Xournal++ use it internally. The poppler-utils package comes with a pdftocairo utility. So the following is just another way to do it in the terminal instead of using a GUI application. Run the following command

pdftocairo -pdf "input.pdf" "output-with-flatten-annotations.pdf"

and your annotations will be flatten/"baked" into the PDF.

But as this more or less a PDF to PDF conversation, some differences may apply, e.g. Poppler considers your fontconfig resulting in font replacements and the internal structure of the PDF may be altered. Please be aware that using poppler-cairo in this context may result in larger PDF output files.

You might also want to try qpdf (another utility and package that is not poppler-related) as that utility does not do an entire PDF conversation.

$ qpdf --flatten-annotations=all input.pdf output.pdf

Please mind that there is also print and screen as argument value for --flatten-annotations= instead of all that includes both print and screen. Check qpdf --help for more information. As the output for help is pretty long, you might want to use a pager like less, e.g.

qpdf --help | less