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It might explain, why we had different results with scribbling/anotating and switching between old/new pdf reader.
It did work for me (I do not use annotations) and did and did not for you. The whole problem might not be switching back and forth 2 readers, but the general issue in in current pdf reader scribbling/annotation export to pdf...
Of course, one never knows, what else is behind the curtain....
I did not look, if the Onyx scrible/annotation system changed since say March 2012. That time the *.sketch files were placed in .Onyx folder which was in folder where was the document (it was not in system part not normaly accessible to user). And so, it was normaly accessable from PC by any filebrowser the same way like the documents.
If one wanted to backup scribles/annot., the best way was to copy the whole folder structure including .Onyx folders.
I one wanted to move doc, say XXX.pdf, including scribles&ann. - doc file and .Onyx/XXX.sketch file have to be moved/coppied.
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