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Remember that when you add books inside calibre it copies them to it's folder. So any change you did inside calibre will not be reflected on your previous folder where you put all of your books. Calibre never touched on the books that were in the folder that ADE used. So if you did some changes with calibre on some books those are still in the calibre folder.
If the files are not in the right format calibre will convert them when sending them to your Kobo. Remember that with calibre and your Kobo plugged in you need to use the send to device button so it can convert the files that are not in a supported format (you might need to set your preferred file format in the preferences->behavior). Also since you added books multiple times check if your don't have multiples books per entry in calibre (Edit metadata look at the top right) and also don't have duplicate entries.
And Forget ADE completely unless you have DRM books. Don't be afraid that your books will get deleted or you won't find them inside calibre. Just backup your entire calibre directory.
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