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You shouldn't need to comment out the first Command resource, pulumi will only run it once provided the inputs don't change.

Commenting it out is expected to delete the resource

In the first phase playbook I have some packages that need to be installed that will take hours . During the 1st phase i comment 2nd phase playbook and same vice versa

No need to do any commenting out.
What you can do is have the 1st command depend on the ec2 instance, and have the 2nd command depend on the 1st command.
This will make it so that pulumi runs everything in sequence, and the commands will only run once on the ec2 instance being created

If it's taking hours to run, it'd be worth creating a golden image for the ec2 instance to use instead of a stock AMI. Tools like Packer can help with this