MichaelH had the right idea with: “Then use the Bulk Delete mechanism to delete 999 tags at a time.”
It’s safe and efficient.
… But I, like others on this tread, want to only delete the tags with low post counts. Unfortunatly, you can’t select “sort by count” on the tag admin page. So here’s how to temporarily hack that functionality:
1) Open /wp_admin/template.php
2) Go to line 721 :
$args = array(‘offset’ => $start, ‘number’ => $pagesize, ‘hide_empty’ => 0);
3) Temporarily change it to:
$args = array(‘offset’ => $start, ‘number’ => $pagesize, ‘hide_empty’ => 0, ‘orderby’ => ‘count’);
This will cause the tag list to sort by count for your bulk deletion needs.
Make sure to change it back when you are done.