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Use the Modify ePub plugin instead of reconverting, far less risk of creating issues with your ePubs.
As for the other part, the easiest way is to just kick off a conversion as soon as Modify ePub has done its work. Also if you have the formats visible as a custom column like I do, then you can quickly see which books only have ePub versions and know that they need converting to mobi. In addition to this I have a "Done" yes/no like Travger suggested.
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