function nightStart(nightNumber, playersArray, roleList) {
  var sheet = SpreadsheetApp.getActiveSpreadsheet();
  var range = sheet.getRange("Controls!G3:G1000");
  var wakeupOrder = [];
  var sleeping;
  var role;

//collecting the array to define in what order roles wake up
  for (var i = 1; i<=20; i++) {
    var cellValue = range.getCell(i,1).getValue();
    wakeupOrder.push(cellValue);
  }

//the FOR loop that I am trying to make work (open Dialog for each role)
  for (index in wakeupOrder) {
    role = wakeupOrder[index];
    if (roleList.indexOf(role) != -1) {
      sleeping = true;
      roleWakeUp(role, playersArray, roleList);
      do {
        Utilities.sleep(2000);
        //calling global sleeping parameter that is defined as FALSE in the 'nightTargetSelection' function
        sleeping = PropertiesService.getScriptProperties().getProperty('sleeping');
      } while (sleeping != false);
    }
  }
}



//below is the function that opens the modal dialog (but the server side code still keeps running).
function roleWakeUp (role, playersArray, roleList){
  //I have removed all code from here for Stack Overflow. The only part that I believe is important is that it opens an HTML dialog with a form
  SpreadsheetApp.getUi().showModalDialog(actionInputDlg, wakeUpText);
}



//Below function is called by the client on HTML form submission. After this form is submitted I need the next dialog to open (i.e need the Utilities.sleep to stop running
function nightTargetSelection (selected, playerNumber){
  var sleeping = false;
  PropertiesService.getScriptProperties().setProperty('sleeping', sleeping);
}

// Open a dialog
function openDialog(jobs, i) {
  var template = HtmlService.createTemplateFromFile('index');
  template.jobs = JSON.stringify(jobs);
  template.index = i;
  SpreadsheetApp.getUi().showModalDialog(template.evaluate(), "sample");
}

// When all jobs were finished, this function is called.
function done(e) {
  Logger.log(e)
}

// Please run this script
function start() {
  var jobs = ["sample1", "sample2", "sample3"];
  openDialog(jobs, 0);
}

<div id="currentjob"></div>
<input type="button" value="ok" onclick="sample()">
<script>
  var jobs = JSON.parse(<?= jobs ?>);
  var index = Number(<?= index ?>);
  document.getElementById("currentjob").innerHTML= "currentJob: " + jobs[index] + ", index: " + index;

  function sample() {
    if (index < jobs.length - 1) {
      google.script.run.openDialog_1(jobs, index + 1);
    } else {
      google.script.run.withSuccessHandler(()=>google.script.host.close()).done("Done.");
    }
  }
</script>