Runner.Stop(true) stops complete execution, not just the current test case

I've faced a similar issue with Runner.Stop(true) stopping the entire execution instead of just skipping specific test cases. What worked for me was using Runner.SkipCurrentTest() within the test case itself, rather than Runner.Stop(true), to bypass only the current test when a certain condition is met. Additionally, I made sure the project playback settings were set to continue running, and the flow control was adjusted in the execution plan to handle such conditions. This way, the rest of the test cases can continue to execute without interruption.

It's probably best to create a new project, with the logic you have defined for Runner.Stop, to see how it works. You can raise an error via Log.Error().

If it's not working as you expect it to be, then it could be an issue with the TC version that you are using.

I'm using this in my tests...

function EventControl_OnLogError(Sender, LogParams)
{
  // in case of error in certain module, stop logging errors/prevent test to fail
  var testModuleName=Project.Variables.currentTestModuleName;
  if (testModuleName=="ConnectionIsNotPrivate_DISMISS")
  {
    Log.Warning(LogParams.MessageText);
    LogParams.Locked = true; //disables further log messages
  }
}

Basically, it skips the (error) logging in case of error in given module and the test continues with next test module. Hope this helps?  

I suggest you see https://support.smartbear.com/testcomplete/docs/testing-with/running/control-test-flow/index.html