Not reproduced on Xubuntu 16.04, Inkscape 0.91-7ubuntu2 and trunk rev. 14995 (libxml2-2.9.3).
@Mc-, it's weird I can't reproduce with 0.91 since we share (almost) the same Inkscape and libxml2 version (yes, I did move the clone before editing the object in the XML editor).
Not reproduced on Xubuntu 16.04, Inkscape 0.91-7ubuntu2 and trunk rev. 14995 (libxml2-2.9.3).
@Mc-, it's weird I can't reproduce with 0.91 since we share (almost) the same Inkscape and libxml2 version (yes, I did move the clone before editing the object in the XML editor).