R3 is shipped with set of SDK tools which can help achieve the goal by avoiding making SQL changes or building an application to modify RetailPublishingJob config. If you have not deployed the SDK yet please do so now, the SDK can be found on the CD in the Msi\RetailSDK\RetailSDK.msi
It should be deployed by leveraging this command:
msiexec /i RetailSDK.msi directexecute=1
Once the SDK is deployed you will find its files in your Documents\Retail SDK, navigate there and open in Visual Studio the solution Online Channel\Tools\Tools.sln then build PublishingConfig project and run it
The section "CRT Initialization", can be found at top left corner, is what you need, make necessary changes and then click "Save" button. This completes Retail Publishing Job changes, in addition you will need to change Publishing Portal configuration by manually editing web.config file, please find details in the 2nd bullet in previous post - Pointing existing R2 eCommerce to a different CRT DB . Note that you can also use the same way of modifying the job's configuration as described in the post for R2 but in R3, with help of the utility, it just can be done simpler.