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If the config folder does need to be cleared, just rename "/home/<username>/.config/calibre/" from "calibre" to "calibre2". Because backups are better, and it won't hurt. This should come AFTER you check to make sure calibre has been told to set the #genre column as a hierarchical type column, though.
Linux hidden folders are no more hidden than Windows hidden folders. Use CTRL+H to view hidden folders like ".config". Or click Menu ==> View ==> Show Hidden Files in nautilus, and similarly for other file browsers I assume. (Which is actually easier than finding the hidden settings in Windows, which recently became hidden somewhere under system settings in the Control Panel, I believe?)
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