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That's a bug in Inkscape then. Extensions do not run within Inkscape. Inkscape writes the SVG to a temporary file and then Inkscape launches a separate process -- concurrently runs another program as though that program is another user. That separate process runs Python and executes the extension which reads in the SVG and then writes it back out again. Inkscape waits for that separate process to finish and then reads back in the SVG output by the separate process. If Inkscape is then dying, then Inkscape has a bug of some sort. While it's possible that the extension is putting out SVG which isn't what Inkscape wants to see (and may even be bad SVG), Inkscape should not crash. Instead it should report an error message.

So, you may want to make sure that you are running a recent version of Inkscape. OTOH, this may be a new bug in Inkscape. Also, it could be that the extension is putting out incomplete SVG, but I'd have to see the input file fed to the extension by Inkscape to tell. (It's some intermediate form of the SVG file you loaded into Inkscape.) Armed with that input and if there's a problem in the extension, then I could fix that. However, the bug in Inkscape would still remain -- the bug that makes it crash when it sees extension output it doesn't like.