Starx

First, Id’s have to unique in a DOM. On this, case where you are appending multiple sets, switch to class selectors.

Next, your variable number is local and redefined and reset to 1 on every mousedown

var copydiv = $('.maindiv').clone();  
var number = 1; // This was redefined and set as 1 on every `mousedown` 
                // So make it global

$("body").delegate(".imagediv","mousedown",function(event){       
    $(".maindiv").attr('class',"changedmain" + number);
    $(".imagediv").attr('class',"changedimage" + number );
    copydiv.insertAfter("#appendafter"); // You might have to change this too 
                                         // depending if this is repeated too
    number = number+1;
}

Also, It is preferable to delegate using a .on() function

$("body").on("mousedown", ".imagediv", function(event){       
    $(".maindiv").attr('class',"changedmain" + number);
    $(".imagediv").attr('class',"changedimage" + number );
    copydiv.insertAfter("#appendafter"); // You might have to change this too 
                                         // depending if this is repeated too
    number = number+1;
}

Solution:

The problem was with the method used. Elements cloned using .clone() will hold the reference, so instead of adding a new element it will keep updating previously referenced objects.

Here is the solution:

var number = 1; //Our Counter Script

function createDiv() {
    //Lets create a new div, 
             // I mean WHY CLONE AT the first place?? 
             // We are delegating events anyway :p

    $("<div />", {
        html : $('#maindiv').html(), // add the HTML of div we are trying to keep
             // ^ Better used cached 
             //   version is not updated regularly

        id : "maindiv-"+number       // add the generate id number 
    }).insertAfter("#appendafter");  // Now insert it
    number++;
}

$("body").on("mousedown", ".imagediv", function(event){
    createDiv(); //Delegating on all elements with `imagediv` class
});

Demo