If something takes over your instance and you lose ssh, here is a way that you can recover it via Cloud-init (As long as you are using Cloud-Init). Use boot_cmd to recover or undo anychanges that caused this.
Find the instance ID and stop it.
aws ec2 stop-instances --instance-ids i-instanceID --force
Create your file. Use boot_cmd as this will execute on boot every time. See https://cloudinit.readthedocs.io/en/latest/topics/examples.html?highlight=systemd#run-commands-on-first-boot for the details.
Base64 encode it.