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I have set up 2 different managed metadata service applications in CA. Lets call them MM1 and MM2.

In the existing MM1 there are existing keywords which is being used by multiple site collections.

However I have created a new instance MM2 where they keywords have to be separated from the previous MM1.

When I created the MM2 the keywords from MM1 populated. Which is wrong, per the requirements they don't want existing MM1 keywords.

Is there a way so MM2 has no existing keywords from the previous instance?

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When you create the second MMS2, avoid adding it to the default proxy group. If you do, all web apps will have two MMSs, which should be avoided.

My guess is that's what happened in your environment.

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