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Converting the non-DRM ePubs shouldn't be a big issue, I do it all the time using Calibre. As for the rest of your requirements? You can certainly do what you need to do, but the one thing that won't work is you'll lose the cross-device whispersync capability doing it by emailing. The problem is that when you email, the item ends up as a personal document. The workaround I've used is to use Calibre to do the conversion, making sure the [EBOK] tag is set in the MOBI output file, and then use Calibre to transfer the file to my Kindle via USB. This retains the whispersync capability, allowing me to pick the book up on my Kindle Fire and jump directly to where I was reading on my Kindle Keyboard.
There are ways to set up Calibre to enable wireless transfer to your Kindle, using a built-in web server. Just not something I choose to do.
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