Multiple wp_query on archive page

I’m not entirely sure, but it looks like you need another conditional in your filter. Right now, it filters all content looking for category, tag or date that don’t have the nav_menu_item, mvp_projecvts query variable set for post types. Perhaps you could add a filter to check if some variable is set and only filter if the variable exists.

$archive_ok= true;
then in your filter:
if ($archive_ok) { do stuff }
$archive_ok=false;

It’s a clunky solution and I am sure there are better answers, but it might work in a pinch.