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You may want to reinstall KOReader from the OCP and then update it. If Nickel had a chance to scan the koreader directory before the ExcludeSyncFolders line was added to Kobo eReader.conf, when the line was added or of the line was removed by a sign out/factory reset, any images, etc. that were scanned in would be deleted.
In Kobo eReader.conf, you should see a line under the [FeatureSettings] header that resembles the line below (I added the |(screensaver_old) segment to keep the screensaver directory from being scanned when I disabled the screensaver.)
[FeatureSettings]
ExcludeSyncFolders=(\\.(?!kobo|adobe).+|([^.][^/]*/)+\\..+)|(screensaver_old)
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