CK Editor - All breaks disappeared?

The BBCode filter should not have anything to do with linebreaks I think, I'm assuming you mean the 'line break converter' filter.

If you were using the 'line break converter' filter on your input format (transforms \n into <p> or <br />) you will get problems. If there are are only linebreaks (\n) in your source, any WYSIWYG editor will simply treat them as source formatting just like the browser does. The WYSIWYG editor will correctly insert <p> or <br /> tags where appropriate and only use linebreaks for its own source formatting, as they will normally not be visible when the node is rendered. But, if you've previously used the 'line break converter' filter, the editor does not know where you actually wanted break/paragraph tags and just treat it all as one big paragraph. It gets a whole lot worse if you have the 'line break converter' filter active when using a WYSIWYG editor. Then both the break/paragraph tags inserted by the editor, and the source formatting linebreaks (converted to break/paragraph tags) will be visible in the rendered node.

So, when using a WYSIWYG editor turn of 'line break converter' and use the editor to insert breaks/paragraphs where you want them.

If you have tons of content already using an input format where 'line break converter' was active (and thus contain no <br>/<p> tags), you might want to keep the converter filter on, and use the helper-module developed in #513998: Plugin to convert p- and br-tags to newlines. (Don't know if it fully works with CKEditor yet.) Note that doing so will add an extra step to the text processing on the client. Your original content with only linbreaks will be converted to using break/paragraph tags before being passed to the editor, and the edited content will those tags replaced by linebreaks when retrieved from the editor. Thus your content will still be saved without the break/paragraph tags in the database and rendered as having them when the node is viewed thanks to the 'line break converter' filter.
There's an open issue [with a workaround/patch] in Drupal Core about that filter not being able to handle very large text in all circumstances though.

The bbcode filter also handles newlines and I was using it to filter all newlines to br, with no p at all.

Anyway surely there's a way to get the editor to insert \n instead of p or br?

Also according to ckeditor's official website it can use bbcode as well. I also have a ton of content in BBcode, not looking forward to rewriting everything.

I didn't realize the BBCode module also handled linebreaks, thought they left that up to the builtin Drupal filter.

CKEditor does not support BBCode by default (the string 'bbcode', or variations of it, does not exist in the entire source tree). One must write a custom Data Processor to explicitly handle BBCode (and most likely also deactivate the supplied HTML Data Processor). We currently override two methods of the Data processor to let Drupal plugins access the WYSIWYG area's [X]HTML, but that should not cause a problem if another Data Processor is used. Some Drupal plugins might expect the 'raw' data format (not the XHTML representation in WYSIWYG mode) to be XHTML as well, but those plugins would just have to be deactivated.

I'm afraid you'll have to stick with FCKeditor (or any other editor supporting BBCode) unless you have more luck than me and find a BBCode plugin/Data Processor for CKEditor.

Thanks, gotcha.