Wordpress - How to use $wpdb to delete in a custom table

You should use the delete() function to remove a row.

A small example to delete the raw 'ID' in the custom table 'eLearning_progress'.

$id = 0815;
$table = 'eLearning_progress';
$wpdb->delete( $table, array( 'id' => $id ) );

But I Can't see which raw you will delete in your table 'eLearning_progress'? Maybe you enhance the question to understand it much better.