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The reason of this problem is because “UpdatePanel completely replaces the contents of the update panel on an update. This means that those events we subscribed to are no longer subscribed because there are new elements in that update panel.”
There is more than one solution to solve this problem:


Solution 1:
Use pageLoad() instead of $(document).ready. modify the code like this :


function pageLoad() {
            $('.bs-pagination td table').each(function (index, obj) {
                convertToPagination(obj)
            });
        }



Solution2:
re-change the style after every update. We can do this by adding these lines to the bs.pagination.js file:


var prm = Sys.WebForms.PageRequestManager.getInstance();

prm.add_endRequest(function () {
    $('.bs-pagination td table').each(function (index, obj) {
        convertToPagination(obj)
    });
});

I'll update this post and the github readme file to include these solutions.