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I spent many hours editing a PDF file and saving it repeatedly in Xournal. I did save it as a PDF file, once at some point so I was able to save some of my work. I then closed the Xournal file, and after reopening it the PDF background was gone, only my text changes remained. Picture first a normal blank fill-in form (a job application) in PDF format. After saving and reopening, picture a blank white page with sporadic typing. Ubuntu 12.04.
Any clues how I can merge the original blank PDF with my typing saved in Xournal format?
This happens to me when the original pdf has been 'locked'.
Often pdf's from banks are in this state.
You don't notice it when editing, only when you re-open the edited file.
I now use APDFPR running in Wine to unlock them before I edit them.
One idea tht might work if you have the .xoj file is to open if for editing with a text editor (eg with kwrite or gedit): you will see inside the name and path of the (locked) pdf. Replace the name with the unlocked pdf.
Note that you will also see in there the text you have entered.
Apologies, I do not know what to do if you have exported it to a .pdf.
The reason it is called "export to PDF" and not "save as PDF" is precisely that afterwards you can no longer re-edit things or recover the original xournal annotations in an editable form. As in most other applications that offer an "export" feature, "exporting" gives you a file you can take somewhere else but loses data in the process. Unfortunately, up to version 0.4.7, exporting fails silently on encrypted PDF files when no password is needed to open the file but a password is needed to modify it. I expect that the new version 0.4.8 released yesterday fixes this problem (but will let affected users check whether it does work properly for them).
The normal workflow is really to work on a .xoj file, and when you want to send the finished product to someone, export it to a PDF, but keep the original .pdf and .xoj files around. Xournal is not a PDF file editor, it's a notetaking program that can work on top of a PDF file -- there's a big difference.
If you still have the .xoj, as pointed out by "undecidable", all you would need to do is replace the original .pdf by a re-distilled version (e.g. using pdftops then ps2pdf, or something similar); or re-open the xoj file and export via Print -> Print to File instead of Export to PDF.
PS: if you send me the .pdf and .xoj files I'm happy to try fixing things for you. Obviously, only send them to me if you're comfortable doing so (e.g. please don't send me your bank information or other confidential documents!)