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You can certainly keep a portable install around and point it to the same library if you want to use the plugin for docx. calibre's db format has not changed in years, so it should be safe. That said, keep an eye on the changelog to see if there are any db format changes. If you want to be absolutely secure you should probably write a bat script that does the conversions using the portable install and updates the epubs in place in the main library.
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