The version 4 series of CKEditor is now supported and it is strongly recommended to upgrade if you are using CKEditor 3.
Beware that CKEditor 4 includes a feature called "Advanced Content Filter" (ACF) which, when enabled limits, and adapts the original markup in a field when the editor is loaded. Please take a moment to look over these settings to avoid potential data loss due to some tags getting removed by the filter.
ACF is independent from Drupal's serverside text format filtering, which only affects content during rendering and it is intended to protect from potential risks such as Cross Site Scripting (XSS) attacks if the editor is initialized with unsafe contents in the original field.
More information about this feature can be found at http://docs.ckeditor.com/#!/guide/dev_advanced_content_filter and the settings to configure ACF can be found under "Cleanup and output" when configuring a CKEditor 4 profile.
