1. What do you mean by the “motion media?” Did you expoort anything from Motion or was the project embedded in the FCP sequence?
2. Have you tried making a duplicate of the sequence, applying the cc filters, saving, and seeing how it opens in Motion?
Generally speaking it is never a good idea to upgrade systems in the middle of a project.
Jim Kanter,
Digital Film Institute
http://www.dfilminst.com