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Dont know how KOReader connects wirelessly to calibre. The upcoming changes will affect only USB device connections, basically they do nothing new (barring some minor improvements and the ability to edit KEPUB) compared to the deprecated plugins. They just improve the out-of-the-box experience of using Kobo devices with calibre and mark me taking over maintenance of the kobo subsytem in calibre which was languishing without a maintainer for a wihle.
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