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Annotations that you made with the standard pdf-viewer can be merged using xournal, but there are some limitations. Xournal only merges correct if the pdf-format that is used is less or equal to PDF-1.4 (Acrobat 5.x). The PDF version is shown in AcrobatReader using File->Properties.
Depending on the PDF-language-features used, some higher version documents can also be converted correctly, just try before you annotate.
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