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 I have 5 vms to be replicated one by one manually, If I add the 2nd vm to protection domain and take the manual snapshot, will it take only chnages and 2nd vm or it will take completed 2 vms again

If you add a second virtual machine to an existing protection domain. The first replication of that second vm will be a full sync. The snapshot of the already added vm will be a changes only.

The snapshot of the already added vm will be a changes only. this will apply to manual snapshot also?

I have to take manual snapshot after adding the 2 nd VM, so it will take full snapshot of only second vm?

yes, as the first vm is already replicated to the other side. 

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