When ever I open Sigil I get a blank file too. I'm pretty sure that's the default. I don't believe Sigil is set up yet, to open the last file you were working on. So I always have to pick it off the File menu, which does list the most recent documents.
But when you double click on an epub file, if Sigil is associated with the epub extension, it does open the requested file. Though it still opens the second blank file too. You may want to post this as an issue with John, the author. It's something he could probably fix. Or if nothing else, he could add it to his todo list.
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