Save as many pickables as you want to

First of all, I would advise you to check out PlayerPrefsX. It's just like the PlayerPrefs within Unity, but it allows you to save booleans, arrays, vectors, etc ...

Now, I would do something like this, have a save function that you can call, and save a value into it:

 function Save(object : String, value : boolean){
 
     PlayerPrefsX.SetBool(object, value);
 }

Then, whenever your player picks up a key, you can do this:

 Save("key_name", true);

Example:

 //Don't have
 Save("key1", false);
 //Do have
 Save("key2", true);
 //Do have
 Save("key3", true);
 //Don't have
 Save("key4", false);

And if you do want to use arrays:

 SaveArray(KeyIDs[], KeyPickUp[]);
 
 function SaveArray(object : String[], value : boolean[]){
     PlayerPrefsX.SetBoolArray(object, value);
 }

-------- UPDATE --------

Okay, so you have your keys all over your map okay? So what you need to do is reference them in your script when you have picked them up.

So, I'm guessing you have a script that allows you to pick up your key? And I'm guessing your keys have a Unique Object name? So not, then do that first; So all your keys are named like 'Key_1', 'Key_2' ...

Then, within your pick up script, you want to do something like this:

 // we do not have any of the keys
 var key_1 : boolean = false;
 var key_2 : boolean = false;
 var key_3 : boolean = false;

 if(pickedUp.transform.name == "Key_1"){
    key_1 = true;
    Save("key_1", true);
 }
 else if(pickedUp.transform.name == "Key_2"){
        key_2 = true;
        Save("key_2", true);
     }

If you want to load if you have your keys or not:

 function Start(){
    key_1 = PlayerPrefsX.GetBool("Key_1");
    key_2 = PlayerPrefsX.GetBool("Key_2");
    key_3 = PlayerPrefsX.GetBool("Key_3");
 }

---------- UPDATE 2 ----------

Or, if you are comfortable with using arrays, you can do this:

 //Place all your keys from the scene into here (via Inspector)
 var KeyObjects : GameObject[];
 //Make all these false from the inspector
 var KeyHave : boolean[];
 
 function Start(){
 
     KeyHave = PlayerPrefsX.GetBoolArray("KeyHave");
 }
 
 function OnCollisionEnter(hit : collider){
 
     for(var i = 0; i < KeyObjects.length; i++){
 
         if(hit.colldier.transform.name == KeyObjects[i]){
 
             print("We have just walked over key: " + KeyObjects[i]);
             KeyHave[i] = true;
 
             //Saves all the keys value
             Save("KeyHave", KeyHave);
         }
 
     }
 }
 
 
 function Save(name : String, value : boolean[]){
 
     PlayerPrefsX.SetBoolArray(name, value);
 }