What is the proper way of updating `Command` section when using SAM

Hi

i'm using Cloudformation and SAM for deploying project infrastrcuture.
While using CommandRunner custom resource I faced with an issue of updating/adding/removing `Command` section.
So it fails to deploy infrastructure with updated `Command` section with `Status reason: The following resource(s) failed to update: [CommandRunner]`

The only workaround right now is to comment/uncomment `AWSUtility::CloudFormation::CommandRunner` in a template every time I need to make a change.

Can you please clarify on the flow I have to follow.

Start by reproducing the update, addition, and removal of the Command section in a SAM/CloudFormation template using AWSUtility::CloudFormation::CommandRunner. Compare the deployment behavior with the comment/uncomment workaround and document the required update flow or the conditions causing the resource update to fail.

Written by the indexing model from the issue text.