I have been applying all the CF updates as they come and never run across this issue before, so posting in case it helps anyone else out.
After running the updater for 12 from the command line -as we have the server locked down- on my Dev box, the folder was no longer there. Interestingly though, the last backup, named 12017ckeditor, was still in the directory.
I figured this was good motivation to get 4.7 up and tested in dev, did so, fixed my other issue (multi-line titles in CFchart), and deployed the update on my production server.
I again saw the ckeditor folder deleted from CFIDE\scripts\ajax. Copied over my new version from Dev and all is well.
My only convern would be if this is a trend in updates to remove unexpected items it will make keeping the bundled components updated a more gruesome task 😕
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spitch, note that in CF2016 (but not 11) Adobe has removed FCKeditor in favor of CKeditor, as of its update 2.
While FCKeditor remains in CF 11, this may be something related to their preparing for a switch in CF11 (per some future update) to CKEditor. It may be that the removal of the folder (as you had placed it there) was done by update 12 as some leftover part of their backing out such a planned move to it. And your one put there got removed because they presumed any there was one they put there.
You could file a bug report at tracker.adobe.com (and you may find that someone else has already reported the same).
But the bigger take away is that since Adobe is moving to CKEditor, they may soon have it there (as they do in CF2016 as of update 2, and they do then REMOVE the fckeditor folder). So you may soon (in 11) not need to add it yourself.
Of course, that's a two-edged sword. You refer to liking to have the latest and greatest ckeditor, and Adobe of course will move MUCH slower to implement new versions of the library. You may be tempted then to just overwrite the one Adobe does place there, but just be sure that neither you (NOR ANYONE ELSE WITH CFML CODE ON YOUR SERVER) uses features of CF that rely on ckeditor (primarily the cftextarea richtext editor), because if you update the library it could cause CF's expected use to break.
Hope that's helpful. It's definitely NOT an official answer.