The original cocos2d-iphone repo has been updated with a 64 bit fix. The version is called 2.2
The fix is a file-by-file replacement of the original 2.1 core API. To update, replace the libs/cocos2d folder, with the cocos2d folder from the download.
By replacing all the files in libs/cocos2d, any user changes made to the API, will of course be lost.
If you have made changes to the 2.1 you are using, you will thus have to update things manually.
The fix can be found here