Reading CheckMark State

You don't need to do that. The thing is, though, that checking the reply itself seems to generate an new, separate reply annotation...

I create a file with a comment and a reply and then checked the box of the reply. I then ran this version of your first code on it:

this.syncAnnotScan();
var annots = this.getAnnots()
for ( var i= 0; i< annots.length; i++) {
    console.println(i+1);
    console.println("Type:"+annots.type);

    console.println("Text:"+annots.contents);

    console.println("Reply:"+(annots.inReplyTo=="" ? "false" : "true"));

    states = annots.getStateInModel("Marked");

    if ( states.length > 0 ) {
        for(j = 0; j < states.length; j++) {
            var s = states.state;     
            console.println("State:"+s);
        }
    } 
    console.println("-----");
}

The results were:

1

Type:Text
Text:master comment
Reply:false
-----
2
Type:Text
Text:reply to master comment
Reply:true
State:Marked
-----
3
Type:Text
Text:Marked set by Gilad
Reply:true
-----

As you can see there are now two "reply" annotations, one that has the actual text I added, and another one that contains an automatic text that is generated when you check the box.

The weird thing is that only the first one has its state set as "Marked"... Another weird thing is that if I delete the master comment and the reply, that third one still remains, even though the Comments list is now empty.