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Disabling the path removal before launching Sigil from the Open With plugin corrects the issue. So far in opening, editing and validating 10 epubs, I haven't had an issue with Sigil so looks as if that code is not needed for Sigil 0.9.0.
One note is that I am—probably—one of the few people who drag Calibre's Book Detail pane into non-existence so right clicking on the format in that pane to launch Sigil is not an option without adding what I consider to be a waste of precious screen space back into view. As usual, YMMV.
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