Erroneous SQL catches too many keys

$custom_sql = "SELECT user_id, meta_key
						FROM " . $table_new_prefix . "usermeta
						WHERE meta_key
						LIKE '" . $old_table_prefix . "%'";

$meta_keys = $wpdb->get_results( $custom_sql );

I think there’s a bug there.

$old_table_prefix almost certainly contains an underscore (e.g. wp_).

So the resulting SQL contains: LIKE ‘wp_%’

However an underscore in MySQL is a one-character wildcard. The above SQL will catch all entries beginning with ‘wp’, not just those beginning with ‘wp_’. You need to escape the prefix first.

https://www.ads-software.com/extend/plugins/change-table-prefix/