I use Calibre as a means to keep track of the books I've gotten from the library. As you've discovered, the books cannot be opened with Calibre, but all the info about the book can. What I do is, when I download a book from Overdrive, I do not use the "open with" dialog. I just save the download to my desktop. This only downloads the licensing info of the book, and when I drag that to Calibre the title shows up and I am able to change the metadata within Calibre. Then I open Adobe Digital Editions and drag the download to it, and then the book is there ready to be transferred to my reader.
I do this with Overdrive audiobooks as well. Can't open anything with Calibre of course, but at least it gives me a way to organize the titles and see what I've already read/listened to.
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