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You could put the files/folders you don't want scanned into a "hidden" folder, one that has a name that starts with a dot/period like ".kobo". Most reading programs can be set to see hidden files/folders. Programs that directly open a file naming the path, including the hidden folder, can do so even if the file is "hidden".
In Windows you can make hidden folders with the command line "md" command or in Windows Explorer you just make the name with a dot before and after the name (.foldername.) and the trailing dot will disappear leaving the hidden folder (named .foldername)
Luck;
Ken
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