I've added some custom functionality to the CKeditor in my admin panel where, rather than using the standard image plugin to embed images in the editor, my users can simply click an image thumbnail on the page, which calls the image plugin and it is automatically inserted into the editor at the current cursor position.
This setup has worked great for a while now, only now I've upgraded to v4.1 and encountered an issue in that, because I don't have the image plugin included in the editor toolbar, any images embedded in the content are removed when the editor intializes. I can still insert images with my custom code, but when I save the page content and reload, the editor automatically removes the images from the content.
This happens to all elements that are not included in the toolbar - if I remove the Link plugin from the toolbar, links are stripped from the content, as well as tables, etc.
I don't know if this is a bug or a feature, only that this behaviour wasn't present in 3.x, which I just upgraded from.
Is there a way that I can force CKEditor to allow these elements even if they are not included in the toolbar? I can use CSS to hide the image icon in the toolbar, but I'd rather disable it at a configuration level.

Check out datafiltering.html
Check out datafiltering.html in samples folder.
I think you just need to define the extraAllowedContent value.
CKEditor 4.1 is a major
CKEditor 4.1 is a major version that introduced a totally new feature called Advanced Content Filter. There was plenty of information published about it so it is a bit surprising that you upgraded to the new version but somehow ignored every piece of communication around it. In any case, a good starting point is the release blog post, there are further links included in it that should explain ACF and its consequences (the ones that have just hit you). See also this blog post: http://ckeditor.com/blog/Upgrading-to-CKEditor-4.1
Documentation Manager, CKSource
See CKEditor 5 docs, CKEditor 4 docs, CKEditor 3 docs, CKFinder 3 docs, CKFinder 2 docs for help.
Visit the new CKEditor SDK for samples showcasing editor features to try out and download!
Our framework uses probably
Our framework uses probably ten dozen different plugins at some point of operation or another. I simply do not have the resources to track updates and release notes for every single one of them.
Simply saying, "That's a new feature, try doing a search for 'Active Content Filter'" would have accomplished much more, without the condescending attitude.
Thank you, handitan, for pointing me in the right direction. I was able to solve the issue.