No warning when opening the same file with 0.91, and using 0.91 to generate the calligraphy files with the inkscape-docs automated process works as expected.
So at least we have a workaround. Now I'm going to investigate if the warning can be fixed in the faulty file or if the bug is in Inkscape itself.
Opening calligraphy-f07.svg generates the following warning (repeated about 30 times):
** (inkscape:30309): CRITICAL **: SPObject* SPDocument: :getObjectById( const gchar*) const: assertion 'id != NULL' failed
No warning when opening the same file with 0.91, and using 0.91 to generate the calligraphy files with the inkscape-docs automated process works as expected.
So at least we have a workaround. Now I'm going to investigate if the warning can be fixed in the faulty file or if the bug is in Inkscape itself.