How to include the same menu twice in a .tpl file
You can probably use the show() function to un-hide the previously rendered element:

&lt;div class="region region-header"&gt;
&lt;div class="hamburger-menu hidden-md hidden-lg"&gt;
    &lt;span class="hamburger-btn"&gt;&lt;/span&gt;
    &lt;?php print render($main_menu); ?&gt;
&lt;/div&gt;
&lt;div class="logo-wrapper"&gt;
    &lt;?php print render($content); ?&gt;
    &lt;?php show($main_menu); ?&gt;
    &lt;?php print render($main_menu); ?&gt;
&lt;/div&gt;
&lt;/div&gt;