Contact Tabs links gone away When clicking on Pager Next/Prev/Page Change under My Custom Tab for Contact
I have found the Problem, Problem was inside pager.tpl
pager.tpl generate some js to handle ajax page loading When pager.tpl location variable != top
That's js look like this without compiled(in pager.tpl):
{if $location neq 'top'}
  &lt;script type=&quot;text/javascript&quot;&gt;
    {literal}
    CRM.$(function($) {
      {/literal}
      var
        $form = $({if empty($form.formClass)}'#crm-main-content-wrapper'{else}'form.{$form.formClass}'{/if}),
        numPages = {$pager-&gt;_response.numPages},
        currentPage = {$pager-&gt;_response.currentPage},
        perPageCount = {$pager-&gt;_perPage},
        currentLocation = {$pager-&gt;_response.currentLocation|json_encode},
        spinning = null,
        refreshing = false;
      {literal}
      function refresh(url) {
        if (!refreshing) {
          refreshing = true;
          var options = url ? {url: url} : {};
          $form.off('.crm-pager').closest('.crm-ajax-container, #crm-main-content-wrapper').crmSnippet(options).crmSnippet('refresh');
        }
      }

      ...

      $form
        .on('click.crm-pager', 'a.ui-spinner-button', function(e) {
          var $el = $(this);
          // Update after a short delay to allow multiple clicks
          spinning !== null &amp;&amp; window.clearTimeout(spinning);
          spinning = window.setTimeout(function() {
            if ($el.is('.crm-pager a')) {
              page($el.siblings('input[name^=crmPID]').spinner('value'));
            } else {
              changeCount($el.siblings('input.crm-rows-per-page-select').spinner('value'));
            }
          }, 200);
        })
        // Handle sorting, paging and alpha filtering links
        .on('click.crm-pager', 'a.crm-pager-link, #alpha-filter a, th a.sorting, th a.sorting_desc, th a.sorting_asc', function(e) {
          refresh($(this).attr('href'));
          e.preventDefault();
        });
    });
    {/literal}
  &lt;/script&gt;

#crm-main-content-wrapper is the main container of All tabs link and tab content. that's why it's html/content replaced by ajax response html.
To fix this what I have done:
Here is my .tpl file code(after fixed):
&lt;form class=&quot;Your_Unique_Class_Name&quot;&gt;
&lt;div class=&quot;view-content&quot;&gt;
  &lt;h3&gt;...&lt;/h3&gt;
  {include file=&quot;CRM/common/pager.tpl&quot; location=&quot;top&quot;}
  {strip}
   &lt;table class=&quot;display&quot;&gt;
    &lt;thead&gt;
    &lt;tr&gt;
        ...
    &lt;/tr&gt;
    &lt;/thead&gt;
    &lt;tbody&gt;

    {foreach from=$rows item=row}
        ...
    {/foreach}
    &lt;/tbody&gt;
    &lt;/table&gt;
    {/strip}
    {include file=&quot;CRM/common/pager.tpl&quot; location=&quot;bottom&quot;}
&lt;/div&gt;
{include file=&quot;CRM/common/jsortable.tpl&quot;}
&lt;/form&gt;

and Code for setting up Pager:
/**
 * Setting up $_pager for pagination support
 * Used CRM_Utils_Pager &amp; CRM/common/pager.tpl to handle pagination
 */
public function pager() {


    $this-&gt;assign( 'form', array( 'formClass' =&gt; 'Your_Unique_Class_Name' ) );


    // Setting up parameters for Pager that we are gonna create
    $params['status'] = ts('Some Entity %%StatusMessage%%');
    $params['csvString'] = NULL;
    $params['buttonTop'] = 'PagerTopButton';
    $params['buttonBottom'] = 'PagerBottomButton';
    $params['rowCount'] = $this-&gt;get(CRM_Utils_Pager::PAGE_ROWCOUNT);
    if (!$params['rowCount']) {
        $params['rowCount'] = CRM_Utils_Pager::ROWCOUNT;
    }

    // Getting all Some Entity by Contact ID. if $_contactId is null then it return value for all Contact.
    $params['total'] = civicrm_api3( 'Entity', 'getcount', array( 'contact_id' =&gt; $this-&gt;_contactId ) );;

    // Setup Pager object and assign into template so it can be used by CRM/common/pager.tpl
    $this-&gt;_pager = new CRM_Utils_Pager($params);
    $this-&gt;assign_by_ref('pager', $this-&gt;_pager);
}

It's taken me long hours to find out this problem solution;
I think it will help you so that's why sharing with you!
Thanks