Disabling a rule in the Rules panel means that the analysis results, that is to say the warning messages, are no longer mapped to it. Initially, the Rule Groups panel displays a disabled rule.
When the project is re-analyzed, warning messages are no longer mapped to the rule, and it is not shown in the tree. The message counts are reduced accordingly.
You can re-enable a rule by right-clicking on it in the Rules panel and selecting the Enable option.