Accessing the EC2 instance even if you loose the pem file is rather easy.
1. First, create a new instance by creating new access file, call it 'helper' instance with same region and VPC as of the lost pem file instance.
2. Now stop the lost pem file instance. Remember not to terminate instance but to stop it.
3. Goto EBS volumes, select the root volume of the lost pem file instance and detach.
4. Now again select the detached volume and this time you have to attach this volume to helper instance which we created before. Since helper instance already has a root volume by default as /dev/sda1, the newly attached volume will be secondary(eg: /dev/sdf).
5. Login to your helper instance with its pem file.
6. Execute below commands:
7. Detach the secondary volume from helper instance.
8. Again attach the volume back to our recovery instance. Start the instance. Terminate the helper instance.
Use helper instance pem file to log into recovery instance.