How can I change the Automation logic without restarting the entire system?

After making changes to an automation module, right-click on the editing area of the module and select Set Online. The edits of that module will be published to the Automation engine and will begin executing without restarting all the modules.
Using Module update by publishing the current module, suspends only the current module, transfers the existing module to the server and resumes the execution of this module. The whole process takes a few milliseconds without interrupting the operation of other modules.