Quote:
Originally Posted by thorgal
... is only a file called sketch or something related to the last file i opened. ...
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Yes, the file *.pdf.sketch contains information about scribbles and annotations you've made in the original pdf. Just try to rename the sketch file which is related to your "contaminated" file (same file name + .sketch).
Edit: I've observed problems with graphics in pdf files. In some cases it takes up to 15 seconds to open the page containing pages with these graphics+text. Taking notes works very very slowly in this case (this bug I want to discuss when the merging bug is solved). Do you have graphics in your document?