There were not sketch files related to "contaminated" files in /.onyx only to the last file i opened (with the old reader btw) which was not "contaminated". Maybe the beta reader stores some info related to the files which has previously opened in another place. In any case the solution i found (changing the name of the document file itself) proves the document itself has not been in any way modified by the beta reader.
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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?
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No graphics (necessarily). It happens the same with plain text small PDFs and large complex documents.