The WooCommerce Wordpress plugin doesn't have a way to update all prices for all products and all variations in bulk. You have to do it by hand, in the Wordpress admin editor, or pay for a "bulk edit" plugin to do it.
Or, you can hack the database directly using some fancy SQL. It took me a while to figure this out.
-- Update all prices for all variations and products that are 4.99, change to 5.99