what font1.defaultLayer[glyph.name] = glyph does: check if the glyph already exists: if it exist it will be removed from that layer: so that the reason why the glyph is at the end of the glyph order in the font overview. (as that glyph is also removed from the glyph order) create a new glyph draw the given glyph in the newly created glyph I cannot reproduce the error, based on your instructions. I will flag this to investigate.