How to retrieve an EC2 Instance with a lost pem file that also have a Self-Managed MongoDB

Steps for connecting to an EBS-backed instance with a different key pair

Step 1: Create a new key pair
Step 2: Get information about the original instance and its root volume
Step 3: Stop the original instance
Step 4: Launch a temporary instance
Step 5: Detach the root volume from the original instance and attach it to the temporary instance
Step 6: Add the new public key to authorized_keys on the original volume mounted to the temporary instance
Step 7: Unmount and detach the original volume from the temporary instance, and reattach it to the original instance
Step 8: Connect to the original instance using the new key pair
Step 9: Clean up

https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/TroubleshootingInstancesConnecting.html#replacing-lost-key-pair

Other solution could be to start using the Systems Manager Session Manager to connect to your instance: https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/session-manager.html