I know this is an old topic but I came across the same issue. I was able to get it to work by modifying the wp-pdf-templates.php file on lines 208 and 209:
$permalink = get_the_permalink() . '?' . $_SERVER['QUERY_STRING'];
$url = parse_url($permalink);
and line 253:
$link = $permalink;
It seems like since the plugin was just using get_the_permalink it wasn’t taking the query string into account at all.
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This reply was modified 7 years, 7 months ago by voltagekc.