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By default, the Wp-PageNavi plugin creates 2 pagination links, from the second page onwards - one at the top, and another at the bottom of the page. How can I disable the pagination at the top, keeping only the pagination at the bottom?
You have to edit your theme.
If you can paste the code of the page in question, i can tell you which part to remove.
if you found something like <?php posts_nav_link(); ?>
make sure to remove it
<?php posts_nav_link(); ?>
have a backup first ;)
Check the plugin settings, but likely it is theme that has call to plugin's function in template or adds it to hook.
Look for wp_pagenavi() call in template or add_action with it in functions.php.
Required, but never shown