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I opened a pdf file in xournal and edited it using a stylus. After saving as a xournal file,with .xoj extension, I selected export as .pdf from the file menu.

When I went to open the new file in pdf viewer and in xournal, all that was visible were the editing marks I had made, and none of the original document.

I'm using ubuntu 16.04.

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Instead of opening the .pdf file directly, I selected "annotate pdf" from the file menu. That opened a dialogue box that allowed me to choose the file to edit. Once done, exporting as .pdf resulted in the complete file - original and edit - to be viewed.

(Leaving this here in case anyone else runs across this problem.)

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Press Ctrl+E to export as a pdf format.

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