one of the easy way to achieve this :-
As you already have two hidden fields but must add runat
attribute to it ,so that
you can get their values at server side. Let's Say:-
<input type="hidden" id="hi1" value="D:\\ProvaUpload\\1.tif" runat="server" />
<input type="hidden" id="hi2" value="D:\\ProvaUpload\\2.tif" runat="server" />
and Make a hidden button :-
<asp:button id="btnhidden" runat="server" Text="hide" Onclick="btnhidden_Click" Style="display:none"/>
Now you can click the button in javascript function :-
function UploadFinished()
{
//your JS code:-
// After finish uploading ..Click the button .. i have used jquery for simplicity:-
$('input[id$="btnhidden"]').click();
}
Now in your code behind :-
protected void btnhidden_Click(Object sender,EventArgs e)
{
// you can get hidden fields values here ....
string val1=hi1.Value;
string val2=hi2.Value;
// Call your merge function here :-
mergeImages(val1,val2);
}