Ignore sticky posts if post is not in meta query

Custom queries and sticky posts are quite a curve ball to work with. I don’t know how your setup looks and what exactly is your user case, but your best solution here would be to run two queries here, the first one to get your sticky posts and the other one to display normal posts

Your first query’s arguments will look something like

$args = array(
  'post_type' => 'myposttype',
  'posts_per_page' => -1,
  'post__in' => get_option( 'sticky_posts' ),
  'ignore_sticky_posts' => 1,
  'meta_query' => array(
  'relation' => 'AND',
   array('key' => 'routeFrom','value' => 'rome','compare' => 'LIKE'),
   array('key' => 'routeTo','value' => 'paris','compare' => 'LIKE'),
   )    
);

Your second query arguments you will need to exclude these stickies

$args = array(
  'post_type'=> 'myposttype',
  'posts_per_page' => 10,
  'post__not_in' => get_option( 'sticky_posts' ),
  'meta_query' => array(
  'relation' => 'AND',
   array('key' => 'routeFrom','value' => 'rome','compare' => 'LIKE'),
   array('key' => 'routeTo','value' => 'paris','compare' => 'LIKE'),
   )    
);

Just make sure that you reset both queries.

As I said before, I do not know your exact setup and user case, but if this is suppose to be the main query, you should look at pre_get_posts to alter the main query accordingly. If so, look at this post I have recently done to include sticky posts outside the home page.

EDIT

I totally forgot to add ignore_sticky_posts to the first set of query arguments. It should work now. I have updated the code accordingly

Just one or two notes on your code

You should use wp_reset_postdata() to reset your queries, not wp_reset_query(). The latter is used with query_posts which you should never use. Also, wp_reset_postdata() should be used between endwhile and endif
To exclude the sticky post query from paged pages, simply warp the code in a if ( !is_paged() ) { YOUR STICKY POST CODE } condition

EDIT

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