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To replace the key pair of a running instance, the following steps must be followed :

1) Go to AWS Console and create a new key pair

2) Generate a public key from the recently generated private key

3) Copy the generated public key into ~/ssh/authorized_keys of server

4) Delete the previous key from  ~/ssh/authorized_keys of server

5) SSH into the instance using the new key

Hope this works!

In case, there is still some confusion, refer to this video on creating EC2 instances :

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