EC2 instance disappeared and not accessible (not visible in terminated or stopped as well)

Which API is CloudTrail showing as returning that error, meaning the eventSource and eventName properties of the CloudTrail event?

If the service is ssm.amazonaws.com (AWS Systems Manager), then the first things to check would be that the EC2 instance is running, which you can check in the AWS Management Console under EC2, and that you're making the API call for SSM in the region where the EC2 instance resides.

If the instance is in the "stopped" state, for example, SSM would report that it's in an invalid state for the SSM Agent on the instance to accept requests, simply because the agent software can't be running while the machine is powered off. If the instance isn't showing in the EC2 console at all, then first check the region selection in the console. You can also use the EC2 Global View option in the console to have it scan all the regions in the world and report which of them contain EC2 instances or other resources.

Is it the instance itself you want to recover, or just the EBS volume?