Probably not the most beautiful and it'd become very long if more than two are needed, but this is A solution.
So basically i create two localStorage and I first check if they are empty and if the key isn't the same as per the variable I am setting, and do this each time I load the page.
if(!localStorage.getItem("idA")) {
  var thisId = "<?php echo $id; ?>";
  localStorage.setItem("idA", thisId);
  console.log("A " + localStorage.getItem("idA"));
} else {
  console.log("A " + localStorage.getItem("idA"));  
}
if(localStorage.getItem("idA") != "<?php echo $id; ?>") {
  if(!localStorage.getItem("idB")) {
    var thisId = "<?php echo $id; ?>";
    localStorage.setItem("idB", thisId);
    console.log("B " + localStorage.getItem("idB"));
  } else {
    console.log("A " + localStorage.getItem("idA"));  
    console.log("B " + localStorage.getItem("idB"));
  }
}
UPDATE
Based on Keith Answer, to add unique values (see this reply on SO), this is what I did:
var thisId = "<?php echo $id; ?>"; 
var lines = localStorage.getItem("lines") ? JSON.parse(localStorage.getItem("lines")) : []; 
var myIdString = JSON.parse(localStorage.getItem("lines")); 
lines.push(thisId); 
function unique(list) { var result = []; 
$.each(list, function(i, e) { 
  if ($.inArray(e, result) == -1) result.push(e); }); 
  return result; 
} 
console.log(unique(lines));