It's important to remember that if you had used (and configured) the native Kobo Touch support prior to installing Kobo Touch Extended, that the upgrade to calibre 8.x would have copied whatever had been configured for the Kobo Touch driver.
So if you had originally configured Kobo Touch to create sub-folders, then installed, configured and used KTE, calibre 8 would have used your original settings from Kobo Touch.
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