ipn.php needs to be accessible
(https://support.wp-pizza.com/paypal-gateway-extension/)
you need to speak to your host and/or check other plugins you are using that might deny access to that page.
might also be a file permission problem.

>Nothing has changed with our site and we have started getting these errors and missing orders
that isn’t really likely . things do not stop working by themselves . maybe some server side software update… but i cannot tell you. I know nothing about your server