[geek1011]

I would suggest the following steps, for now (until I finish the plugin, which won't be for a bit):
1. Backup the calibre library (after closing calibre)
2. Delete all .kepubs
3. Run kepubify on the calibre library folder
4. Batch rename the outputted .kepub.epub s into .kepub s (but keep the directory structure)
5. Merge the converted folder into the calibre library one
6. Start calibre again

I would do it this way, as as davidfor said, you can cheat and replace the books. Kepubify is also fastest when converting multiple books all at once. Also, this way needs the least scripting and is pretty simple.