В основном события DOM перезаписываются, поэтому вам нужно использовать setTimeout в afterLoad для решения проблемы:
$("#id_of_fancybox_thingy").fancybox({
//all your existing stuff goes here...
afterLoad:function(){
setTimeout(function(){
if (CKEDITOR.instances['elementname']) {
CKEDITOR.instances['jelementname'].destroy();
delete CKEDITOR.instances['elementname'];
}
CKEDITOR.replace('elementname', { "toolbar": [ [ "Cut", "Copy", "Paste", "PasteText", "PasteFromWord", "-", "Print" ], [ "Undo", "Redo", "-", "Find", "Replace", "-", "SelectAll", "RemoveFormat" ], [ "\/" ], [ "Bold", "Italic", "Underline", "Strike", "-", "Subscript", "Superscript" ], [ "NumberedList", "BulletedList", "-", "Outdent", "Indent", "Blockquote" ], [ "JustifyLeft", "JustifyCenter", "JustifyRight", "JustifyBlock" ], [ "Link", "Unlink", "Anchor" ], [ "\/" ], [ "TextColor", "BGColor" ], [ "Maximize", "ShowBlocks" ] ], "height": "200", "width": "690" });
}, 1000);
}
});