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There was only a trace amount. It had little to no effect on Kakashi's Kamui.The fact that the cloak never vanished from the alliance until the God Tree was cut down is evidence enough. Go and re read chapter 644. You will see then that the cloak had never vanished from the alliance. When Minato mixed his chakra with Naruto's everyone's cloak came back to them without Naruto even touching them because it never left to begin with and all the ninetails chakra is connected to itself so their cloaks became even more powerful than before because now it was full (yin+yang) ninetails chakra.