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In the dropdown in the Kobo Utilities configuration, you can add/remove profiles and select what devices the profile applies to. I would suggest looking at your profiles in the dropdown and seeing what changes this makes to the device selection, custom columns and store on connect settings. If you want to remove a device, that's on the second page of the configuration pages.
The settings I use automate the storage to calibre but you will need to manually restore them from the Store/Restore Current Bookmarks tool.
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