Whew! That's a weight off my mind.
I'll take a look at the calibre plugin when I get some time, to see if there's a workaround. This issue (or previous ones similar
to it) is why I stopped using that plugin (for Sigil and epubs, anyway). I thought that calibre had added some kind of permanent (not a plugin) feature to do the same thing as the Open With plugin that didn't suffer from this issue, though.
EDIT: It's still there (and still works). When you do View->View Specific Format, the Choose Format dialog has an "Open AZW3/EPUB/MOBI with" dropdown--depending on which format is selected--in the bottom left-hand corner) that will allow you to configure applications to open the various formats with (and will remember those applications). Might not be quite as easy, but it does work.