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So you have a current collection with data in it - server A.
You have another collection with some of the same data, which is
missing some, and which there are some conflicts - server B.
The simplest thing to do is do a mongodump from server B, mongorestore
to server A.
Then you know that you have a copy of every document (by _id).
Now the question is what do you want to do if there is the same _id on
A and B with different data.
I can help you detect those, but the real question is what do you want
to, as that has to be handled completely by you.