Personally I would just put all my pdfs into a "Hidden" folder and not have the stock software see them at all. (actually I let the stock software see only a few files) A hidden folder is one that the name begins with a dot/period like .PDFs, Koreader can be set to see hidden files. To make a hidden folder, using windows explorer, you just put a dot/period at the beginning of the name and at the end. The one at the end will disappear leaving you with the hidden folder. Any sub-folders, to a hidden folder, will also be hidden from the stock processing.
Luck;
Ken
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