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Just put them in a folder/directory that has a name that starts with a period/dot, such as .PDFs or .Library. You can make such a folder, in Windows by Naming it with a period before and after the name like: .Books. , the dot after the name will disappear leaving you with .Books, the files and subfolders you put into that folder will not be processed by Kobo. KOReader and coolreader can be set to read such "hidden" files.
Luck;
Ken
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