Is there any word on the ending anime sequence where Lucca finds Kidd? If CC is going to be retconned out, you'd assume they'd have to remove or edit it. However, that Crono and crew fight and defeat the TD doesn't necessarily cancel Chrono Cross. Remember that the TD can only be destroyed, and Schala can only be saved, through the use of the Chrono Cross. Simply defeating it ought to result in it being re-absorbed into the Darkness, like when you defeat it without using the CC in Chrono Cross.