UEFA have said that any agreement between Chelsea and Atletico that prevents Courtois playing, should they draw each other, is null and void as far as they're concerned.
Yep http://www.uefa.org/about-uefa/administration/news/newsid=2088774.html
I'm not sure whether we'd pursue it further but knowing Uefa I wouldn't bother they'll probably end up slapping us with a champions league ban even if I don't think that it is within their remit to do so given this is a contractual issue.