If instance is not ready, the text set would be discarded

On initialization of the CkEditor (version 4 here), you should never set any data before the editor is ready to handle it.

// Initialize this._editor with replace

if (this._editor.status !== "ready") {
    this._editor.on("instanceReady",
        event => {
            event.editor.setData(data);
        });
} else {
    this._editor.setData(data);
}

Hope this helps someone.

I also load a page snippet with CKEDITOR functionality via AJAX and as such I have experienced many of the problems outlined in this question. This is my solution:

function setCk(id){
if(window.CKEDITOR){
    var _instId = CKEDITOR.instances[id];
    if(_instId == undefined){
        CKEDITOR.inline(id);
    }else{
        CKEDITOR.instances[id].destroy();
        CKEDITOR.inline(id);
    }
}

}

On each AJAX response for this snippet I inject a script element into the head with a call to setCk(textareaId). The trick being to destroy any previous CKEDITOR instances for the target ID & re-initialise CKEDITOR after each AJAX snippet load.

//creating instance of ck-editor
var yourInstance = CKEDITOR.instances.yourContainer;
//check instance of your ck-editor 
if(yourInstance){
      //destroy instance
      yourInstance .destroy(true); 
}
// create instance again
CKEDITOR.replace( 'yourContainer' );