Greetings!
I don't recognize that link you gave: http://next.ohloh.net/projects/3200
The domain name 'next.ohloh.net' doesn't seem to exist for me.
As far as moving the repositories, Ohloh should be smart enough, yes. Each commit has a unique identifier and even if you move to a different repo, that commit ID should remain the same, so when Ohloh crawls the new one it should see commits it already has and not pay attention to those ones.
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