This was done because Apple has chosen to make content blocking unavailable to third party browsers on iOS. (goodereader.com)
i've read that flash is going to be integrated into chrome on jelly bean, if flash is not gonna be compatible for 4.1, then third party browsers won't have flash at all unless they integrate it as well.. (tmonews.com)
Third party browser add - ons like SurfCube still work too, meaning nothing seems to have been broken by the update. (windowscentral.com)