Mongodb users in replica
So in your case, currently all the nodes(A, B and C) are running as standalone nodes with a different set of data. 

Now you are trying to establish a replica with the existing nodes.

As per your question, first, you are trying to convert node A to a replica set member and then adding B and C to the replica set. So mostly, in this case, node A will become primary and B and C will be added as secondary. Since B and C are added as secondary for one time it will replicate all data from A. This one time process is called Initial Sync.

When Initial Sync is happening, mongod removes the contents of the dbPath directory of B and C node.

Please follow the steps in Deploy a Replica Set to set up the replica set.

Answering your second question, this procedure will delete all users and data from Node B and C.