I had this problem. What a pain.
To properly destroy the editor instance, try
if (CKEDITOR.instances.myInstanceName) CKEDITOR.instances.myInstanceName.destroy();
From the documentation here
I solved the missing content issue by assigning the contents of the editor to a hidden field prior to postback. I'm using ASP.Net, but it should work universally.
in the client-side click handler of the submit button, call
if (CKEDITOR.instances.myInstanceName)
document.getElementById('hiddenField').value = CKEDITOR.instances.getData();
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