Comment 3 for bug 642417

Please keep the issues separate - I didn't mean to tell you to download and compile Inkscape 0.48 just to get an updated version of a single extension script file, even more so as it is unclear what the actual cause of your problem is.

When exporting your SVG file to XCF using Inkscape 0.47 (and Python 2.6.2) on Mac OS X 10.5.8 I get the same deprecation warning but the XCF file is saved nevertheless. It is however empty, because all the drawing content is outside the page margins.

If I resize the page to the drawing contents the file exports to XCF as expected (attached file was exported with Inskcape 0.47).

It seems your issue is with the installation or system configuration and not with a specific Inkscape version.