Your best solution is to keep all of your eBooks in ePub. You can convert the ones you want to KF8 for your wife's Kindle. You can use the KoboTouchExtended driver to convert your ePub to KePub on the fly when you send them to one of the Kobos.
There's no need to keep KePub in the library. That's why the driver does the conversion on the fly.
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