I use both Calibre and Ebook Library and have only had problems when I used the Sync option. I use Calibre to make conversions and to add missing book covers, etc., and then I upload the files to Ebook Library where I use the bookmarks/highlighting options to make initial notes. In these scenarios, Ebook Library has worked fine,
as long as I don't ever Sync.
In Calibre's defense, it is an excellent piece of software that Kovid is constantly updating and supporting. I don't think anyone (even Sony) would consider you a "Bad Boy" if you used it.