I don't have multiple copies of Sony Store ebooks on my Windows PC. I get a single .epub per ebook in My Documents\My Books\Reader Library. However, I don't have a Sony Reader - so perhaps the other files are related to your Reader.
In any case, except for Google ePubs, these almost always have DRM (encryption), so they can't be converted by Calibre.
As Madam Broshkina said, the Nook can read ePubs with Adobe DRM. The only trick is to register your Nook to your AdobeID. For details, see
How to read Adobe PDF and Adobe ePub books. Once the Nook is registered, you can either use Desktop Adobe Digital Editions to copy the epub, or just copy it over yourself to the "my documents" folder on your nook.