could you try this (use have_rows and a wile loop instead of your foreach loop) :
<aside class="widget">
<?php
if( have_rows('tool_section_links') ):
echo '<h2>Tools</h2>';
echo '<ul>';
while( have_rows('tool_section_links') ): the_row();
$show_desktop = get_sub_field('show_desktop');
$tool_link = get_sub_field('tool_link');
$tool_link_title = get_sub_field('tool_link_title');
if ($show_desktop == 'yes'){
echo '<li class="show-for-large-up"><a href="'.$tool_link.'">'.$tool_link_title.'</a></li>';
} else {
echo '<li><a href="'.$tool_link.'">'.$tool_link_title.'</a></li>';
}
endwhile;
echo '</ul>';
endif;
?>
</aside>
depend on witch fieldtype you use change if ($show_desktop == 'yes') to correct value
