Your Kobo eReader.conf file probably has a line like this:
Code:
ExcludeSyncFolders=(\\.(?!kobo|adobe).+|([^.][^/]*/)+\\..+)
You could edit it like this:
Code:
ExcludeSyncFolders=(\\.(?!kobo|koreader|adobe).+|([^.][^/]*/)+\\..+)
Put all your books in the .koreader folder, and now Nickel shouldn't try to index them anymore.