Per default the cleanup process of edit-on Pro removes all elements and attributes which are not included in the XHTML Transitional DTD. By setting the "dropillegalattributes" and "dropillegaltags" attributes of the cleanupprocess to false, you can prevent the removing of custom elements and attributes:

....
<cleanupprocess cleanuponload="auto"

cleanuponsave="auto" dropillegalattributes="false" dropillegaltags="false" />
....

If you do not want edit-on Pro to remove your custom tags and attributes, but to remove all other tags and attributes which aren't included in the XHTML Transitional DTD, you must create your own DTD containing your custom tags and attributes, see FAQ