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Unfortunately, there are no calls to comment and uncomment assets within a BlPackage.
Alternatively, you can do this:
Create a new package in a temporary directory through the script with the assets you wish to deploy and Update your existing package with the temporary package. You can use the following blcli calls:
1. Create Package (there are several create package calls; Be sure to use the one that caters to your requirements)
2. updateByName / updateByDBKey - You can use either one of these calls to update your existing package with the new package you created in step#1
3. deleteBlPackageByGroupAndName - Use this calls to delete the temporary package you created in step#1
This should help you get the right contents into BlPackage everytime you want to deploy.